The heaters will always be on, a half power switch wouldn't turn those off, not in a JSX anyway. There is no power half power switch on the JSX anyway as it happens.
The filament supply in the JSX has a 10A fuse in it and all the filaments (for the power valves at least) will be in parallel, so there shouldn't be an issue with the filament voltage itself. Since if the fuse clearly hasn't blown and since some valves are being heated.
Some valves I think do glow a bit dimmer than others and I don't think looking at the filament glow is the best way to diagnose a fault (unless the filament clearly isn't glowing). You can get blown valves with perfectly fine bright filaments. I've seen quite a few! I'd suggest moving the valves around but if you do have a valve with a short in it you can potentially cause extra damage to other screen grid resistors, which is something I found out the hard way in a 5150.
Even if you took two valves out and ran it at 50 watts I'd still expect it to be plenty loud!
This might seem like a silly question, but did you have the loop engaged? and if so, where did you have the effects send and return levels set?