We tried to reproduce this but couldn't. Please note that server restart procedure withing VisualCron is the same as stopping the VisualCron service and then start it again. So you should be able to reproduce this quickly if there is a problem.
Please check the following:
1. try creating a new folder "settings2" in VisualCron folder
2. change server settings folder in server settings to that folder
3. add a new fake credential with local logon and load profile checked
4. write down a credential that has these checked as well
5. stop service
6. start service
7. restart client and connect
8. double check that new and old settings are there
If not, there might be something with storing the settings folder and we will proceed to that test.