Sometimes you have to watch out how fast you freeze unicellular organisms. I have not froze yeast yet but I am a microbiologist that works on other eukaryotic unicellular organisms.
The idea of storing organisms in a freezer is to slow down the metabolic pathways. The problem with freezing living things is that ice crystals can form and rupture the cell. Things like glycerol and DMSO allow ice crystals not to form as much as only using pure water.
While these help reduce ice crystals, they do not eliminate them. One problem could be the speed of freezing, two, the amount being frozen at a time, and three, the final freezing temperature.
To address the first problem I suggest freezing the vials you are storing very slowly. When I freeze my organisms I put mix the cells in a cryoprotectant and then put them in this container called a
Mr. Frosty. It is ridiculously expensive for what it is. Basically it is a plastic container that surrounds the vials to be frozen. Inside the plastic container you put in isopropyl alcohol to allow the box to slowly freeze. This helps reduce the formation of ice crystals. Maybe get some kind of rack to hold the vials and then put them in a container filled with isopropyl alcohol. Let it sit in the freezer for 1-3 hours and then take out to freeze normally.
For the second potential problem, I suggest buying the right kind of
cryotubes (not class or weak plastic). Get the ones that are not too large. You want to freeze the smallest volume that is economically feasible. I would freeze in 0.5 to 2-mL cryotubes.
Three: The final temperature you are freezing could also play a role. Usually the lower the better. I will look through some methods of long term yeast storage to find out what is common to use. Things like bacteria are stored at -80 degrees Celsius in a glycerol mixture. Also, if you freezer's temperature is fluctuating as can occur for defrosting home freezers then your yeast may die or be seriously affected. The idea for freezing is to stop metabolic activity in the cells without killing them. If you thaw the vials and then refreeze then it is possible (if you have not killed them ) that you are selecting for strains that may not make the best beer.