Indeed. I suspect memory leaks related to market actions too. And I always play on Linux, and it was with 2.5 already. It is most noticable when transferring alien materials or antimatter. Saving and relaunching often increases speed greatly. Perhaps it's related to switching through bases while the market view is open.
So, take valgrind and find it.
EDIT
Btw, watching the page file grow in task manager is a good indicator as well.