Can you explain what your workflow is, what program is adding the logo, what type of file, where LR Import and Export are in the process, etc?
One common workflow would be to import original photography into LR, make adjustments, then set your logo PNG that you’ve previously created in PS with transparency, as a graphic watermark in the LR Export panel and export the photos. That simple process is working as far as the watermark being applied during export, as far as I know, in both LR4 and LR6.
I am importing a jpeg logo, LR requests a jpg or png, using the import logo feature in the file export and watermark panel in LR.
For years it worked and now over the past three months things have gone south.
Lightroom does not put the watermark on the thumbnail/preview image in the JPG, only the full-size image, so depending on what and how you're viewing the images, you may not see it, if the viewer isn't showing you the fullsize image. If you export your images smaller than the screen, then the file-viewer is likely to show the full-size image.
If you want you can upload both the logo and an exported jpg to www.dropbox.com and let others look at it, and try using the logo in case something is corrupted about it.
Also make sure that the path to the logo jpg has not changed since you created the preset and/or recreate the preset just to make sure.