There are no limits (as far as I am aware) to the number of custom filters that the extension can handle. What version of Adblock Plus do you use? Does chrome://adblockplus/content/errors.html display anything?
Yes, this is most likely a localStorage limitation, which has become problematic in this - hopefully rare - because all locally-cached filter lists count toward this limit, and deselected ones are not deleted. We don't currently use the unlimitedStorage manifest.json permission, which would solve this (but I don't know if enabling it result in a potentially confusing 'new permissions' dialog box in Chrome - Wladimir, any thoughts?).
Here is a workaround: Tools -> Extensions -> Developer mode, then under the ABPC entry, click "background.html". Then in the window that comes up, click Resources, Local Storage, then the entry under that that just appeared, then delete all the local storage entries that start with "http". Sorry this workaround is so convoluted...
Sorry, I mistakenly posted information pertaining to the Firefox version of Adblock Plus - I had forgotten the forum that I was in and how different the Chrome extension is.
Guess I missed that part, sorry. I suppose we'll need it at some point though, or hopefully the Chrome folks will allow it to apply to localStorage at some point in the future.