Yes, those are usually the most difficult cases to solve. NOT_ECLIPSE.
Recently two bugs has been opened, which consumed significant amount of our time:
Bug 103301 - [Webapp] Search highlighting hangs for awhile on some pages in Internet Explorer
The title of bug clearly indicates that it is not Eclipse issue. Opera, Firefox and Chrome work fine, only IE displays information that the script is long running and whether you want to cancel it. This issue is almost impossible to reproduce without knowing search query and specifically structured help page.
This bug has been workarounded by adding timeout to the script when running on IE.
Bug 279440 - Invalid warnings when using windows offline synchronization
Maybe not all of you know, but Windows allows for accessing files from network drive even if you are offline. Those files are just kept somewhere in the cache and synchronized when possible. Now if you try to keep your project on such a network drive, can you imagine that Eclipse prompts you that your file has been modified by external tool after every save? More, if you try to reload the file, you may lost your changes. The issue is caused by the fact that Windows needs a lot of time to notice that file has been changed and to update a timestamp. So if you write anything to a file, then read its timestamp, and read it after some time, they will be different. This could not be fixed :-(.
BTW. Recently we had Galileo Demo Camp, please expect some news today.