Delay compensation not working
 

I find delay compensation in Pro Tools not working properly. I have 2 kick tracks perfectly aligned. With delay compensation off they add up perfectly, the same when they have the same plugins in chain but when I deactivate one, there is phase misalignment, level drops and low end is gone. I work in 2018.1 but also downgraded to 12.8.3 to check if there is any difference and there's not. Can someone explain how should I use delay compensation to get most of it?

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looks like it's DeBleeder - when switched in bypass PT doesn't set delay compensation well.

Re: Delay compensation not working
 

This is the issue between deactivate verses bypass.
This has been an "issue" for a long time (and sometimes has been used to an advantage if you know what is going to happen) but the simplest instruction is you shouldn't use deactivate in general and just use bypass.

Bypass keeps the delay in the channel in because of the ability to immediately un-bypass. Technically, a bypassed plugin should not be compensating for any delay since the plugin is not in the loop. But if the DAW did this, when un-bypassing on the fly, all the channels would click as they would all have to re-compensate for a new delay in the system. So the delay compensation stays in for a bypassed plugin.

When you deactivate, it's as if the plugin was never there.
So running parallel tracks with one in bypass and one in deactivate is going to cause issues because the actual "fault" is on the bypass track which should have no delay (but can't be done because of the reasons stated above in my second paragraph.)