I asked this question some time ago related to earlier version of Projeqtor but, with 6.3.3 it became much more worse:
What is Projeqtor doing in background after login?
It takes several minutes to have everything loaded. Tested with Firefox.
At login, projeqtor caches some data (for instances most parameters) and calculates access rights.
This may take a while if you are allocated to many (hundreds of) projects. I saw long lasting connection for users allocated to more than 200 projects, just it was about 30 seconds (not minutes).
If it takes very long for few projects, then possibly you have performance issue on your system.