It may be too late but I will still try to answer. Event-based sampling and Statistical Callgraph are based on the different collectors. So, having both checked you invoke two types of collection and analysis. Loop analysis will significantly add to the overhead.
Which collector to start with depends on which information is needed. If you want just hotspot functions to be identified, just use Basic Event-based sampling. If call stack information needed, start with Statistical Callgraph.
The resolving symbols stage could take the significant amount of time depending on the size of the project being profiled.
Do not use loop analysis until you need a clue which of hotspot functions have loops or being called from a loop.
You might want to consider using the command line mode of collection and Eclipse for results viewing. It will separate the bugs of collectors and viewers.
If you consider sending the information regarding bugs of PTU, please include the logs saved in %temp%/ptu-log-