Hi Markus,
Some words of wisdom from someone who manages client sites for a living…hire a techie to sort it out.
You have a fundamental flaw with your service setup. You have reported a lot of odd issues that I have not seen in the 8 years I have managed client sites that include s2member.
You have an extensive plug-in list any one of which could be the culprit.
Your client issues reported are abnormal. That is…there are lots of issues clients report but profiles that disappear should not happen. User accounts and user profiles are a core feature. Plug-ins would need to go out of their way to wipe a profile…seriously troubling from a quality perspective.
Because most, if not all, of your problems reported are intermittent and non-reproducible and you can’t just turn off all the plugins since your live clients would not have a service, you need a techie to decide how to approach this and fix it. It may be deducible from log files or may require the addition of custom logging code. I would be surprised if this was an S2member issue…but…never say never.
Good luck with this one.