William B
you have to put more than one coat, spackel will shrink, when it drys, thats why a drywaller will put on 3 coats ,in a 3 or 4 day period, you better off to put thin coats on it will dry faster and shrink less, compared to a thick coat,

oil field trash
Glass having a very smooth surface, it is not likely that you will be able to use any type of spackle or similar filler. It simply won't grab the surface of the glass. It might appear to be adhering but I believe in time it will flake off. You might try one of the "stick to any surface" primers similar to Kilz.

Yoda
cut small pieces of drywall to fit over glass, adhere to glass with powergrab, then tape and fill the edges with joint compound. Yoda out

cheezy
clean the glass then use the self adhesive mesh type dry wall tape on the glass. this will give the drywall mud something to grab onto. you have to do the mudding one layer at a time, letting it dry completely between layers. if there is room--maybe try siliconing a peice of wood to the glass to bring it level with the wall. then tape & mud the joints & the wood to hide the grain. If all else fails--hang a cool piece of artwork over the whole thing

trampusdog
if i understand this question correctly you are trying to fill your joints not go over your blocks . if this is right you need to clean out what you put in and use a clear glass sealer / adhesive it is sold where glass blocks are sold .it comes in tubes you can remove the joint compound by using warm water and a putty knife.