Thank you for your patience! Skuid has fixed the issue you raised regarding Lightning Design field misalignments (issue DSC-1318) in the 12.1.1 (and later) releases.
As a reminder, Salesforce does NOT allow reverting back to prior versions of managed packages. Skuid always recommends installing new versions in a non-business critical sandbox environment to test all mission critical functionality before installing into a production environment. We also recommend that you update out of date themes after you upgrade. Please let us know if you continue to encounter any problems with this issue after upgrading.