could this be another 'amp-in-the-room' versus 'close-mic'ed-amp' issue?
you cannot really compare a Profile taken from one amp with another amp (same model & make) and expect them to sound the same, since the cabinet, mic and the placement of the mic play such a huge part.
are you experienced with close mic'd amp sounds, as you would have in a studio setting, where the amp sits next to you but the speaker is in a booth far, far away and you only hear the mic'd signal over the studio monitors?
if you want 'amp-in-the-room', play the PROFILER over a guitar cabinet (OUTPUT section, page 1, enable 'Monitor Cab Off')
close mic'd amps have A LOT of aggressive high end in them, either place an EQ in the EFFECTS section and set 'Low Cut' and 'High Cut' (page 4/5) to taste, or try the 'Pure Cabinet' feature.
Also, if your monitoring over headphones, enable 'Space', OUTPUT menu, page 5/7
hth