upgrade breaks localScale and prefabs

i've got a project i've been working on for a few months and i've gone through upgrades before with a few hiccups but nothing like this. i have a couple simple prefabs (one sphere and one more complex spaceship) and when my scene loads i instantiate them both into planets and the spaceship. when making the planets i make them different sizes so in the script i set their transform.localScale accordingly. the problem is with the recent editor upgrade the scaling is either off or the prefab is not importing properly. the result being i would need to either re-engineer the prefabs and/or adjust the scaling i'm using for pretty much everything. i guess my question is has anyone else experienced this? it is worth noting that i'm building the entire project bootstrap style with no objects existing until the bootstrap script is loaded (it loads everything from camera to environment). it is also worth noting that i have tried to revert to the previous version of unity and load a (git revisioned) copy of the project with no luck. thank you in advance for any feedback.