@nickw I have seen this "System cannot find the drive" message before. May be a bug - need to look in our ticketing system.
There is a new protop 319 that was released this week. I suggest you try that first. Simply run %PROTOP%\bin\pt3upd from ProEnv.
The DBAnalysis file has to be in %PROTOP\dbanalys and named nick.dba. But if you did it from ProTop RT then it should be fine. That msg may be from before you run DB Analysis.
The "Creating new flag" is normal. All ProTop processes use a file named %PROTOP%\tmp<something>.flg to signal their existance. The easiest way to stop a ProTop process is to simply remove the associated flg file.