I have recently also ran into this issue and was able to narrow down what was causing it (at least for me).
My project is saved as a project and in that project folder I have a "REFERENCES" folder.
In that folder I have pictures, Word documents, PDF's, Excel documents, etc...
Construct 2 would save but it felt slow. (I would have a bunch of the documents from the "REFERENCES" folder open)
When I had an Excel document open from that "REFERENCES" folder and tried to save my project it would freeze up.
I tried this with other documents but so far it's only happening with open Excel files.
Once I moved the "REFERENCES" folder outside of the project folder it no longer froze and was actually much faster in saving.
Hope that helps.