Are you using wildcard projects ? How many files do you have actually open? That is, how many files are restored when you open the project? Look at the Files tool window / Buffers.
You can profile where it is spending time by closing the workspace, then going to Macro > Start Slick-C Profiling, then re-opening the workspace, then going to Macro > Slick-C Profiler > Save... to save the results of the profiling session.