Sam,
I see this sliding down the list, unanswered. I don't have a Maxitrak Allchin or experience of, I do have a Dixie loco though and have worked on a 3" Maxitrak Avelling. Standard gauge glasses on those worked but were rather a small diameter so didn't work as well as they might have.
Not sure exactly what you mean in your question? Are you saying you get a "bubble" under the expected level of the water or does the water disappear from the glass and not come back? What happens if you open the blow down, does the water disappear and then bounce straight back up when you close it? That would be the normal scenario if all passages are clear. You say you have checked for blockages and can't see any? Have you taken the fittings off the boiler and made sure there is no scale built up in either the fittings or the tappings in the boiler? Have you blown through both top and bottom fittings and made sure there is no restrictions?
With a proper 3 cock glass you would close both cocks to the boiler and open the blowdown and drain the glass to make sure both valves to pressure close off, then with the drain open open the water (lower cock) and make sure you have a good flow, you can tell by the sound what the flow is like. Then close the water valve and open the steam valve and make sure you have a good flow of steam, this will sound markedly different, higher in pitch. Then close the steam valve, close the blow down and open the water, water should go right to the top of the glass, then open the steam valve and the water should drop to the correct level. Finally open and close the drain and see the water bob down and then back up the glass. Unfortunately I suspect you have only a blow down so you can only do the last test. If the water does not disappear and return quickly then I would suggest one of the fittings to the boiler is blocked. You only have steam or water to play with when its in steam, no air!
Worth noting an incline (or decline) can have quite an effect on water reading. A trick from the old time enginemen when going down hill and the water disappeared from the bottom nut was to haul back on the reverser to slow the engine to get the water surging back and forth in the boiler to give an idea of the real level. One "mistake" of inexperienced drivers when the water reading was fine on the level is to top the boiler up when going down hill to bring it back up the glass (often causing priming) and then when they start up the hill the other side of the down grade there is a lack of steam space, lose pressure and more priming! Always good to know where exactly the water level is when on the bottom nut of the gauge in relation to the firebox crown, then you know what your margin is and when to panic!!
Good luck,
Paul.