I have both resharper 2.0 for vs 2003 and 2.5 for vs 2005 installed. I notice they share the same configuration files in \Application Data\JetBrains\ReSharper2\.
This cause one bug: After I open vs 2005, the IntelliSense is reset back to "Visual Studio" and "Color identifiers" is unchecked in vs 2003. After I open vs 2003, then they are reset in vs 2005. Since I have to work on both version of visual studio quite often, every time I have to re-select these two options.
These are only two issues that I noticed since I used it every day. Maybe there are other options that have similar problem.