A/DA Flanger high pitched squeal

[BDuguay]

Desperation bump.

[DrAlx]

I don't see how comparing voltages between two circuits is going to help you.
You are not going to "see" that whine as a voltage reading.
Even if you do find a difference in measured voltages between the two circuits, you are not going to know if that is the actual cause of the problem, or an associated side-effect, or even if it is remotely relevant.  Not posting a schematic for the actual circuit makes it hard to guide you.  The only thing I can find is a Moosapotamus clone with no IC types marked, so no idea what your pin 14 actually refers to.  The one pin 14 that I see seems to have its voltage set by the manual control, so maybe voltage difference is OK.  Repeating my previous advice...  ***Audio probe*** to find where the noise appears. 

[Fender3D]

LM324(d) provides a voltage to achieve the manual function.
This voltage depends on Manual position...

This voltage might be an issue only if it's rising while squealing...

Please,

...we should first realize what is the noise, I mean, if it is a clock issue or not,
check VCO frequency(es) and supply voltages

[DrAlx]

If it is clock noise, you would most probably hear the squeel if you audio probe one of the BBD clock lines, but I would only probe those if you found noise was present at BBD output but not BBD input.

One other (obvious) thing to point out is that when you audio probe you should do so with any feedback/regeneration switched off.

[BDuguay]

Audio probing will be a bit of a challenge because the squeal eventually goes away. It looks like I have no choice though.
Thanks for the input everyone!
B.