Not to suggest there may not be some other issue at work --issues can and do occur with botched installations or corrupted tools-- but Zbrush and Zbrush files do also become less stable when handling especially dense subtools, or files where the the total size exceeds a certain threshold. This is usually due to the accumulation of geometry, or “tons of subtools.” This threshhold will vary with the system, but I generally start to purge before exceeding a few GB.
Remember that saving a project file will save every tool loaded into the session. If you only need to save the active tool, save it as a tool instead in the Tool > Save As menu.