No brakes when engine is running

[CK9404]

Here's what I got.
87 1/2 SWB with light duty brakes and the 305
Little Shop rear disc swap kit
POL Corvette style MC and proportioning valve (disc/disc)
New factory replacement power booster
I replaced the front calipers and all the rubber lines last year. I have replaced the rear hard lines and one of the front hard lines.
Here's the problem
Brakes have been gravity bled and then 2 man bled with no air coming out. There are no leaks. All connections have been double checked and torqued down tight.
I have a good firm pedal and good fluid flow at all bleeders. Whenever I start the truck and it gets vacuum the pedal basically disappears. Still get fluid moving but the pedal is basically just flopping there.
I have tried two of the same MC and reinstalled the factory booster and no change.
I am at a lost and need help.
Thank you!

[Shifty]

First thing that comes to mind is the booster check valve.  Plug it off (both sides), and see if the pedal still sinks when you start it.

[CK9404]

If I pull the vacuum line out of the booster while it's running the pedal is fine

[bd]

Whenever I start the truck and it gets vacuum the pedal basically disappears. Still get fluid moving but the pedal is basically just flopping there.

Expand on these comments ^^^^^.  What do you mean, "...the pedal basically disappears" and "...the pedal is basically just flopping there?"  Does pedal firmness go soft?  Does the truck stop like it should?

[CK9404]

Yes the pedal is soft, very soft. I have not driven it yet. I have it on a lift at the moment. Trying to solve this before I put it on the road

[Shifty]

If I pull the vacuum line out of the booster while it's running the pedal is fine

Are you losing brake fluid at all?  If so, the master cylinder is probably leaking from the seal(s) on the piston into the booster. 

If not, it's probably a bad booster or check valve.  Remember, when carrying the booster to and from, don't carry is by the pushrod, it will tear the diaphragm. 

[bd]

If the brake pedal becomes "softer" with the engine running, then the booster is doing its job.  Removing the vacuum source from the booster by disconnecting the vacuum check valve simply defeats power assist. 

You could bench bleed the M/C and re-gravity bleed the calipers if there is concern over the possibility of air in the system.  Otherwise, remove the vehicle from the rack and perform a very conservative and cautious stop test and driveway check.  Remain alert, drive slowly and very cautiously, at first.  If the truck stops properly, the soft pedal may be a normal symptom of proper power booster function.

You need to determine whether you are attempting to solve a problem that doesn't exist or you may wind up with ulcers from worry.

[CK9404]

Not losing fluid at all. I pulled the new booster to swap back to the old one. I inspected for fluid loss and there was nothing in the booster.
It's hard to explain that when I say the pedal is soft, I mean it totally goes away. I can literally take my hand and flick it and it will go to the floor, but only when there is vacuum.
I also swapped out the MC and rebled it.
I am not a mechanic but I do know when something isn't right and this is not right
I have not messed with the check valve. I don't see how it would effect it this much

[bd]

I can literally take my hand and flick it and it will go to the floor, but only when there is vacuum.

That certainly makes the problem clearer.  Do the brakes drag excessively or lock up when the engine starts?

[CK9404]

They do not.

[Mike81K10]

If the MC was not bench bled prior to install, it should be. I think you have a lot of air in the system.

[JohnnyPopper]

If the MC was not bench bled prior to install, it should be. I think you have a lot of air in the system.

I think Mike is correct. Compressing air is the only thing left.

[Shifty]

I'm not familiar with this rear caliper kit, where are the bleeders on the calipers?  They will be a mutha to bleed if they are up top, ask me how I know.

[VileZambonie]

If everything is installed correctly and your pedal free play is in spec, then your issue is the setup. You will need to switch to a quick take-up master cylinder.

[CK9404]

The MC was bench bled properly.
Everything I’ve read is that the bleeders are supposed to be at the top of the calipers. Otherwise you can get air pockets
Not familiar with the quick take-up MC