Your rabbit likely has cecal dysbiosis, caused by a disruption to the normal microflora in the rabbits cecum. This is most commonly due to diet issues from too many sugars or carbohydrates(grains, fruit, high starch veg like carrots, other sugars) in the rabbits diet, which will also include pellets or other rabbit food mixes, as they have added grains and sugars usually(unless plain hay pellets with nothing but hay and no other additives). But sometimes cecal dysbiosis can also be due to a sensitivity to a particular food. Pellets and/or treats will most often be the culprit, but sometimes it will be a particular veggie or even sometimes certain types of hay can cause issues, especially rich leafy hays or grain hays.
Usually the best way to correct cecal dysbiosis is by an elimination diet. This is best accomplished by removing all other foods and only feeding grass hay. Usually any variety of grass hay is fine, preferably one that is an even mix of leaf and stem. You want to free feed it, meaning your rabbit always has hay available to eat, all the time. When doing this diet though and removing veggies and pellets/mixes, you have to absolutely ensure your rabbit is eating the hay really well, and eating lots of it to make up for no veg or pellets in the diet, or your rabbit could actually starve itself. So your rabbits eating has to be very closely monitored for the first couple of days, then generally monitored after that to ensure that a good amount of hay is being consumed each day. So doing this elimination diet, this means grass hay only and absolutely no pellets, no veg,
no grains, especially no corn, no treats of any kind.
I'm not sure what type of grass hay you have available to you where you live, but it needs to be a very good quality hay(no mold) that doesn't contain noxious weeds, and hasn't been wet since it was dried and baled so it won't contain mold. You will also need to be careful that no harmful chemicals were used in any part of the growing/baling process. Usually a good quality horse hay works well for rabbits.
When doing this elimination diet, you need to closely monitor your rabbits weight to ensure that your bun stays at a healthy weight and doesn't get too skinny. Depending on how bad the cecal dysbiosis is and how long it has gone on, it can sometimes take several weeks to months of a grass hay only diet before you start seeing a significant improvement and the problem starts correcting itself. This is because the good microflora in the cecum has to reestablish itself, and grass hay is usually the best tolerated food for rabbits and helps to reestablish this microflora. Usually you will see some improvement within a couple of weeks though, and sometimes the improvement will happen within a few days.
Once you no longer see the mushy poop and it has been cleared up for several weeks, you can start to gradually add other foods back into the diet. I prefer to start with dark leafy greens and/or other forage like rabbit safe leaves and plants. When adding in these items, always start with one item at a time and in a very small amount. After at least 3 days on the small amount(meaning a small sprig or small piece of a leaf) if you see no signs of mushy poop or other digestive upset, you can start to gradually increase the amount given each day. After a couple of weeks on this new item, if there are no signs of it causing digestive upset, you can add in another new food item and gradually introduce it the same way. And continue on with this process of slow introduction of new foods, so that if you do find a food that causes digestive issues, you know which one is causing the problem and can eliminate it from the diet permanently.
I think it is quite possible that the pellets you have been using are what have caused the digestive upset in your rabbit. If you believe this to be true then either stop feeding pellets altogether and feed only hay, veg, and forage, or find a better pellet brand that won't cause these issues. if you do reintroduce pellets back into your rabbits diet, then make sure to do it very gradually, starting with a small amount and gradually increasing the amount over several weeks. But the fact is you may not ever be able to feed pellets again. I had one rabbit that couldn't have pellets or any other food mixes for rabbits, as they made him sick. He lived on free fed grass hay, dark leafy veg, and forage, and was perfectly healthy on this diet.
Here's some information on cecal dysbiosis and changing the diet to correct the problem.
http://rabbit.org/intermittent-soft-cecotropes-in-rabbits/
http://sawneeanimalclinic.com/downloads/chronic_intermittent_diarrhea_in_rabbits.pdf
http://rabbit.org/disorders-of-the-cecum/
Sometimes something like this can also be caused by digestive disorders such as megacolon or dysautonomia, both of which are usually regulated by diet and sometimes medications like gut stimulants. Usually if it is either of these digestive disorders, the fecal poop will also be abnormal and won't be the usual round fecal poop, but will also be somewhat abnormally formed and irregularly shaped. If your rabbits fecal poop is normal round fecal balls, then these disorders are unlikely and your rabbits problem is likely cecal dysbiosis caused by diet.
http://www.therabbithouse.com/diet/rabbit-droppings.asp
http://www.therabbithouse.com/diet/rabbit-digestive-system.asp
If your rabbit does have abnormally formed fecal poop in addition to the mushy cecotropes, then mega colon or dysautonomia are possible causes. Usually the same dietary changes are needed as you would do for cecal dysbiosis, by eliminating pellets and other sugary/starchy foods, and only feeding a good quality grass hay, and sometimes dark green leafy veg and other forage can be reintroduced into the diet gradually if they don't appear to cause issues. Sometimes prokinetics like metoclopramide, cisapride, or domperidone may be needed along with dietary changes, to help regulate the contractions in the gut and improve gastric emptying.
http://wildpro.twycrosszoo.org/S/00dis/Miscellaneous/Leporine_Dysautonomia.htm
http://www.vgr1.com/megacolon/
To make managing the messy bottom a little easier, if you haven't already I would suggest either having your vet keep your rabbits bottom fur trimmed or learning to carefully do it yourself. I say carefully as rabbit skin is very thin, so you have to take extra care not to accidentally nick it. Your vet should be able to show you how to do this properly. Keeping the fur trimmed short will help so the poop won't have fur to stick to as easily and any that does stick can more easily be cleaned off. Instead of having to wash your rabbits bottom, you may be able to just clean it off with a cloth.
I personally would also want to stop the metronidazole since it's not improving anything, and like any antibiotic can sometimes contribute to gut problems worsening.
Best of luck in sorting this difficult problem out. One other possibility in figuring out what is going on if dietary changes don't help, is if you want to have your vet consult with a rabbit specialist. There would be a consult fee, but it may help you find the answers you need. There are several rabbit specialists in the UK. If that is something you want to look into I could provide a few names and links to their websites.
