Community Store Add-on consuming massive amounts of memory and timing out1 user found helpful
With this setup, just say you have 10 values for the first option, 5 for the next and 10 for a third, you end up with the system trying to handle 10x5x10 variations, so 500 variation options. This generally isn't wanted, you'd just pick one of the options to be in variations, or a few and keep the numbers down.
Until two days ago, this 'In Variations' option for product options was in a branch and not in the master and a release - in those cases the options were _always_ added to variation combinations, resulting in some cases where it multiplied them and made things explode.
With the 1.2 release you should see those options - with the product you are adding/editing, make sure you check those.
Further to that, I have a pull request soon to be merged that aims to make the saving more efficient. Critically though I've put in a limit to the number of variations (50) so that you can't lock up a product. You might want to try just adding in this little bit of code here and seeing if that helps:
If it's nothing to do with product variation combinations I can't really suggest what else it would be, I've not encountered any other timeouts myself apart from that situation.