If lots of presets exhibit the same issue then you need to think about external factors... maybe your room has some resonant peaks in the frequencies associated with 'flub'. Of course this wouldn't apply when monitoring through headphones.
Ultimately there is a list of things to try including the following:
Use different guitars
Try different rooms
Move and adjust the position of your monitor speakers
Compare and contrast with other people using the same preset to obtain a baseline
And.. other 'things'... but more advice will be on hand from others too.
some of the stuff you'd done in the cab block like lower the hi cut and turn up proximity weren't helping
Just tried the settings for the 6550 as Simeon has proposed. Great idea, inspired me to play some good old hardrock stuff for more than one hour. Put a superdrive and a eq (to boost the mids) in front of the amp. Awesome sound, thanks Simeoni can't load the patch, it just comes up with the amp block set to default, but the recording sounds pretty bad
you are using quite a bassy cab, with the proximity turned up
try this
amp - reset it and then
bass 0
mid 8
treb 7.5
pres 7
treb drive 7
norm drive 2
motor drive - 4
cab - reset it and then
F103
some of the stuff you'd done in the cab block like lower the hi cut and turn up proximity weren't helping
it's quite a dark amp that one
keep the same cab and then try the 50w 6550 amp
gain - 6
bass - 3
mid - 7
treb - 7
motor drive 4
here's what the 6550 sounds like to me with those settings
http://simeonharris.co.uk/misc/plexi.wav