Along with the tips in Harm's link and the questions, when you do your Ctrl+S, do you get a small box with a progress bar?
Even with an 8 hour Project with thousands of Assets, located on a FW-800 external HDD, my Saves are only about 30 sec. at the most. Same for the AutoSaves on this monster Project. Now, I do not attempt to do any editing, while that progress bar is up, but would imagine that the program is unusable during that time.
Good luck, and let us know about your system and Project, per the questions in Harm's link.
Project - XDCAM EX 1080 50i (1h video)
Premiere Pro CS 4.2.1, English
Windows 7 x64, English, Just installed, all updates
Intel Ouard CPU 2.4
After saving the project (on same HDD with projects files), a status bar appears, showing the process of saving normaly.
After that, Prime freezes for 1 minute (not responding), then begins to operate normally.
Freezing does not occur when I save the project to another hard disk!
The same freezing occurred during rendering (status bar stops, premiere "not responding" ~for 1 min, then begins to operate normally ) until that time until I moved to another hard disk preview files (using scratch disc).
Looks like a problem with reading HDD.
Answer the remaining questions and in addition tell us your disk setup.