This isn’t an issue with MyEclipse (Eclipse provides the base CVS integration and we have no code that modifies the SC modules in any way). BUT, what I would suggest trying is the following:
File > Switch Workspace > C:\tempworkspace, hit OK to restart. Now setup a new CVS repository to match the one that was giving you trouble, try and checkout and sync with it… is it still slow? If so, thereis osmething wrong with your computer’s setup. Double check your Windows firewall settings (you said it was new, this could be an issue) also check Virus scanners and see how aggressively they are set.
Also do you notice this problem with other CVS repositories as well? Try and hookup to the eclipse.org CVS repo and checkout the source code for GEF or something, did it take a long time as well?