Hi ,
Does this happen when you copy a project from 4.1 and open it with 4.6? Have you tried migrating only the problem assets from 4.1 to 4.6 after opening a copy in 4.6 and deleting the assets that have a scaling problem? Have you tried creating new assets for 4.6 specifically?
Also have you tried downloading the 4.5.1 version of the Engine and seeing if the problem occurs in that version. (You can have multiple versions of the engine installed.)
Please try the above troubleshooting steps and let me know the results.
Thanks.