Hello all!
We're very sorry we took so long to figure out a solution that was so obvious to a problem that frustrated many. If your screen's dimensions are too small to complete the 99x50 (or any other) achievement, you can now select the achievement branch in Steam and get the latest build which will complete any achievement of a size greater than the one you're doing if the one you're doing is the biggest you have available.
This version, however, is VERY untested. The old engine is/was, well, to be frank, a bit of a mess (and this is why you should switch to the newer, shinier, faster, with picture, zoom, etc. InfiniPicross 2.0 :happy_creep: ) and, because of that, it might have issues with the new dev environment, the new java environment, the new packaging method, etc. so only use this version if a) you need the achievement(s) or b) you're aware of the possible issues and want to take a chance on it.
Again, very, very sorry to have taken so long to solve such a fundamental issue. We thank you so much for your time and hope you have fun with the InfiniPicross family!