I've been having that problem with some Humbrol paints (not that they're made by Humbrol these days, heaven knows where it's made!).
I find the only way to solve the problem is continuous stirring, and then use some, decanted into a pallette. Once used, and stirred again, it almost works as it should, although still poor quality, and tends to 'go off' in the tin quickly.
If lacquer thinners has been added, then this could cause pigment and carrier separation when used. Enamel thinners, or a cheaper alternative, white spirit (basically the same thing) should be used.
I contacted Hornby Products well over a year ago, informing them of the variable, and overall poor quality of the paints, noting that this has only happened since the demise of the Humbrol factory - no reply yet received!
I have some original, 'ewal' Humbrol paints which are 30 years old, and still work perfectly.