If anyone is using or has used Adobe Media Encoder v13.0.1(Build12) to transcode media, your transcodes will have incorrect timecode that does not match the original source media.
This was discovered recently and exhaustively tested on multiple computers with various media sources, various preference settings and various AME application files, confirming that all clips passing through this one version of AME consistently have timecode that does not match the original source.
The mess that this creates occurs later, assuming your project is using an offline-online workflow, when you conform your final sequence to the original media. At that stage all conformed clips will be visibly off by some random amount and will need manual fixing.
If you discover that this has occurred in your project, you can manually modify the affected clips by highlighting the clip in your browser and selecting MODIFY->TIMECODE. There you will need to confirm the correct timecode of the first frame of the original source media used to create this transcoded clip and enter that number into the start timecode of this window. CAUTION - this must be done with care, as this changes the timecode of the clip in Premiere AND of the file on the hard drive and it is a permanent change of the file.
If you have a ton of affected clips this is the only option, it's painstaking but will rectify the problem and avoid a potential disaster in conform later.
Subsequent versions of AME no longer have this issue. If you haven't updated AME yet, do so now.
If anyone from Adobe is in this forum and has a comment to share, the floor is yours.