Symptom
A software package which is non virtual may perform very slow.
Solution / Workaround
Even non-virtual application are being redirected through the SVS/SWV Filesystem Minidriver while at least 1 virtual layer is active on the system.
This may significantly slow down applications with many registry/file system I/O operations. (e.g bad performance at startup)
To work around this issue you can add those application to the SVS Program Ignore list which you may find at the following location:
HKLMSystemAltirisProgramIgnoreList (REG_MULTI_SZ)
However bear in mind that those applications will no longer see any virtualized resources.