Nope... I haven't had that problem.
I'm a bit confused with what you mean with "internal clock"... I didn't even know that Model 24 HAD an internal clock. Probably because I never have used it, or needed it.
Maybe you mean your OS's internal clock, or some other midi-hardware clock.
Anyway... I know that from Firmware 1.40 Tascam added:
"A function to output MIDI time code to a computer connected by USB has been added".
I see that you have firmware 1.50... maybe there is some "hickup" in your installation of 1.50? Try to install version 1.60, and see if it disappears!?
Or maybe... if you use a "click-track"... there might be is some unwanted "overflow/bleeding" from that click-track to other tracks?
I don't use a click-track myself so I wouldn't know if it can create unwanted noise on other channels.
I use pre-programmed (programmed by myself) "analogue drums" from Toontrack Superior Drummer 3 as a "click-track". Or more accurately... as a "backing-track" to play along to to get the right "groove" for my guitar/bass/keyboard playing & recording.
A computerized track without "a feeling", and without accentuation, drum-rolls & crash-cymbals etc, and that only says "click-click"... well... it just doesn't do it for me. It only makes my guitar playing stiff & emotionless. But that's me....