It seems phoenix.exe is launched with incorrect parameters (i.e. lacking a space) when fastloop is disabled. In Process Explorer on phoenix.exe (Properties > Image):
phoenix  -u http://user:pass@bitcoinpool.com:8332 -k poclbm VECTORS BFI_INT FASTLOOP=falseAGGRESSION=7 DEVICE=0 WORKSIZE=512 -q 2
This probably causes both the fastloop and aggression settings to not be parsed. For some reason when launching like this (also when launched manually in a command-prompt), on my system the miner only uses up to 82% GPU and thus a lower hashrate.

Tested on: Phoenix Rising 1.3c
Hardware: Radeon HD 6850
Workaround: enable fastloop

EDIT:
On second inspection it seems that FASTLOOP=false is still parsed even if another argument is directly attached to it, so only the aggression argument is ignored. Apparently my card needs fastloop to run at full-speed, so I should have just enabled it in the first place.