If you place a block with light value in the glass bell, it lights up as expected, but if you unload the chunk (quitting, leaving the area, etc.) and return to it, the light will be gone. If you right-click the block and open the GUI, the light updates.

Anyway, I took a quick look around to find the cause. I've never touched tile entity inventory/containers before so I don't really know how syncing for that works, but I think it could be because BlockGlassBell checks the inventory item for the light value, while the packet sent to update the TileGlassBell only updates tileGlassBell.outputItemStack. The only time the inventory gets synced is when you open the GUI (I think), causing it to update the light properly.

I've noticed the same problem. It seems to happen every time the client unloads the area. The area it is in is chunkloaded but every time I come back it's not showing the light.

I'm assuming this is for EE3 in MC 1.6.4? It's been fixed in EE3 for MC 1.7.2 for about two weeks now

Yes, it is 1.6.4.