I have been creating paintings in TSRW for ages, and never have I came across this problem before. I'll give you the steps I always perform ...
- Open up the template I created with a fake mount, with shadowing for realistic effect, and an alpha channel the template is made for the mesh I always use - "teen poster"
- Place each image onto the template, save the texture as .dds and repeat this process for however many images I have
- Open S3OC and clone the "teen poster" mesh.
- Open TSRW and import my cloned mesh
- Delete all existing variations except 1 and make empty.
- I then choose the wood pattern I use for the frame
- Duplicate the empty variation for the amount of Images I have
- Click overlay, edit, import image, click no so it imports as a new texture. I repeat this step for however many I have.
- Export as S3P & Edit project contents and export .package