The 68RFE has two filters - the flat main sump filter, and the spin-on cooler return filter (both are inside the trans). On the first change, did they change both filters? The second time around, did they change both again, or only the main sump filter?
It sounds to me like you're getting converter drainback, where part of the oil in the converter drains back into the sump. This normally causes "delayed engagement" complaints (when first started up cold), although technically this is a misnomer since the trans is engaging just fine, but there is no torque coming from the converter (because it's half full of air). As the converter fills up, the truck kind of "oozes" slowly into gear (or at least, that's what it feels like as the torque comes up - the trans was actually engaged OK all the time).
But another symptom you can get with drainback is momentary loss of prime (loss of line pressure). The return oil from the converter goes into pump suction. If the converter has drained back, then as it refills a slug of air is expelled from the converter, and when this air goes into the pump suction (supply) port, you lose your line pressure briefly. That would give you the "neutral" feel, followed by a "bang" engagement when the pressure suddenly comes back. You should also have a P0944 (Loss of Prime) fault set in the trans controller.
In either case, I'd suspect a bad cooler return (spin-on) filter, especially if it was replaced initially but then left alone on the second repair. The cooler return filter must include an anti-drainback diaphragm to prevent the converter from draining down. If you used an aftermarket filter, you might have gotten one with no anti-drainback diaphragm, or with one that's ineffective. I would recommend using a Mopar cooler return filter. Those should be from the same source as our production filters, and should not give you a drainback problem.
"Normal" drainback (giving you the "oozing into gear" feeling) will not hurt the trans at all, but the loss of prime / "neutrals out" situation can distress your UD clutch, so I would definitely avoid that. You can either replace the cooler return filter, or (as you mentioned) just run it in Park briefly after each cold startup. The converter will refill in Park (unlike the 47RE and 48RE).
