Setting the working directory for the task should not be needed, What specific issues did you notice without this being set?
After further research and investigating I am not entirely sure if FlashFXP should run the scheduled task with the "Run with highest privileges" option set, as this changes the context in which FlashFXP runs.The only instance where I can see this might be needed is when FlashFXP needs to transfer files to/from a local folder that require elevated administrative permissions and even then this could cause additional problems...
Such as.. If FlashFXP is installed with per-user settings then the elevated process would have a separate set of settings vs a copy of FlashFXP run without being elevated.
When you put FlashFXP on the Windows 2008 R2 server did you install FlashFXP? (or did you just copy over the FlashFXP program folder)
From within FlashFXP can you please paste the information from main menu > Help About > Details tab
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