Neural_Override

So I've been trying to figure this one out for a while, and I'm hoping someone here has seen this problem and might know what's causing it. It's a 2009 A4 (B8), with about 56k miles.
When I have the A/C on and I'm driving along, the tach will sometimes (vertical video warning). This happens when I have the pedal down at a static place (not accelerating, just cruising). It also happens at different gears (I've seen it happen on 4, 5, and 6) and speeds (I've had it happen anywhere from 35MPH to 50).
Also, when I'm at a stop and push the gas, the car will hesitate (another vertical video warning). If I punch it to get through the hesitation, it'll actually stall out and I have to start the car again. At least once this has happened, the car didn't start on the first try.
Notes:
Only happens with the A/C on.
Doesn't happen all the time; but when it does it's definitely after the car was been driven for at least 20 minutes. I drive the same route every day; sometimes it happens, sometimes it doesn't.
There doesn't seem to be a direct correlation with how hot it is; could be 75 degrees or it could be 100.
If I turn off the A/C while the tach is skipping, it'll start acting like normal. If I turn off the A/C while it's hesitating, it'll go back to normal. It definitely has something to do with the A/C being on. Also keeping it in S tronic doesn't seem to show either issue (skipping or hesitation); only happens in D.
I've switched to stock in my APR settings, same issue.
I'm now sometimes getting a P0299 (underboost) CEL that clears itself after a bit of driving, but will randomly pop back up. Even when I'm not going close to WOT. This is a new symptom (within the last month or so). I wasn't getting the CEL before while having this issue, so I'm not sure if it's related.
I bought the car in Feb/13, and put APR stage 1 in April. It happened that summer at least once (so it happened before stage 2). Since then (so AFTER the first time it happened) I've replaced the DV with a GFB DV+, added a Eurocode Intercooler Pipe, a 034 HFC, a K&N Typhoon CAI, and bumped it to stage 2.
I've checked for leaks as best I could and everything looks solid.
I know someone with VCDS, but I don't think it's the legit version; it's 12.12, and I don't see boost as an option to log (under 01 - Engine, Advanced Measure Blocks, there's no boost in the list).
Anyone have any ideas?
Edit:
Here's a screenshot of DashCommand.

Kris Hansen

how about in Tip mode? It only happens in D, and only with the AC on? In that first video, there's a kind of a squealing sound while you accelerate, is that actually there in real life?

Neural_Override

Doesn't happen in S tronic mode. If I shift it into S mode (or turn off the A/C), the issue immediately goes away. Even the hesitation from stop doesnt happen while in S mode.
The whistle is coming from the CAI.

Neural_Override

^ Tiptronic. Sorry, I keep calling it S tronic for some reason.

Turbo Freak

Wishful thinking !