What cams do you have? I see your sig says comp but are they a rough idling set of comps?
Rough idling cams will cause flashing O/D light issues with the auto causing it to shift weird. Some know how to tune it out. I'm having this issue with my hot rod cams. Luckily Doug @ Bama knows how to tune it out and I have one of his tunes, but my Brenspeed tune and my BBR tune do it. I'm afraid the "fix" in the tune is just covering up the real issue though.
Also, for me and everyone else pretty much, this only happens under heavy stop and go traffic (where the brake is used a lot) and doesn't matter if I have the O/D turned on or off.
One other guy who has this issue too said he got a P0745 code. This seems to somewhat jive with what Brenspeed told me the flashing O/D light usually means.
I've been trying to figure this out, and I'm really thinking it's a vacuum issue due to these lumpy cams giving you lower vacuum. And since it happens only in heavy stop and go traffic where you use the brake a lot (and brakes use your vacuum), it kind of makes sense. Another guy said this issue is less and less likely to happen if you run a high idle as opposed to a low idle we normally like to run w/ rough cams.

So this really sounds like a vacuum issue to me and somehow, a too low of a vacuum is causing something funny to happen where the line pressure solenoid is seeing a lower than normal voltage, thus throwing P0745. Maybe I'm wrong about all this but it sure seems likely to me. I'm going to be doing more tests to see if this is true or not (I'd be pretty surprised if not).
Of course, your issue may be something else. But I do know now that rough cams + 5r55s = issues and it's common.
I've been working with Justin Burcham of JPC on this issue. I haven't heard back since my last email to him but I'm sure he'll figure out something.