Hi Daniel,
Especially when we upgrade the application we are getting more issues, this i observed so many times and no root cause for this. If we go with fresh installation, the whole environment is working fine. I recommend, if your developments are less, better take back of all content, uninstall old version then install new version freshly.
Before that, check all the EIM APS services in CMC are enabled and running.
Thanks,
Ramakrishna Kamurthy