First at all, I want to know if you tried latest Update 7.
I experienced similar thing before (used early version), I suspectthattarget process is shared by other application. If Hotspots collector dynamically instruments the process (binary) in shared memory, it will cause unexpected results. (not sure if this problem will happen in new version...)
Instead you can lightweight-hotspots analysis will capture performance data in low level and there is no instrumentation. For example: #amplxe-cl -collect lightweight-hotspots -duration 10 -target-process gam-server