I've got this problem when developing Structure plugin integration with GreenHopper. We have included our web-resource, which contains a rather large CSS, to be pulled up within gh-rapid web context.

As a result, JIRA combined all CSS files into one batch:
/jira/s/..../_/download/contextbatch/css/greenhopper-rapid-non-gadget,gh-rapid,atl.general/batch.css

This batch is 18,000 lines long and the number of rules exceeded 4096, which is the limit for one CSS file in IE8 and IE9.

As a result, half of the rules are lost and the application works incorrectly.