It would appear that this part of the help file is incorrect.
Specifically the switch -logfile= is incorrect.
it should be -logpath=<path> and -logopt=00000000
1 = on
0 = off
Each index (1-8) identifies which log file to enable
1. log session
2. log uploads
3. log downloads
4. log fxp
5. log successful (must be combined with 2, 3, or 4)
6. log failed (must be combined with 2, 3, or 4)
7. log skipped (must be combined with 2, 3, or 4)
8. log summary
So to log the session only you would use FlashFXP.exe -logpath="C:\data\logs\" -logopt=10000000