If your source file contains:

• A video watermark effect
• An In point positioned further from the start of the source file than the length of the watermark effect 

Then you might not see the watermark in the job preview or in the transcoded file. For example, if the source file contains a two-minute long video watermark filter and an In point at 3:00, the watermark might not appear.

To correct this issue, transcode the file twice: once to create a movie that doesn't require an In point, and again to add the watermark. Follow these steps:

1. Remove the watermark filter from the original source file. Do not remove the In point.
2. Transcode the batch using a high-quality setting, for example, ProRes 422 HQ.
3. Create a second batch in Compressor.
4. Add the transcoded movie to the second batch. 
5. Add the video watermark to the source file. 
6. Transcode the second batch. 

The second transcoded file includes the watermark effect. 

To learn more, read about using In and Out points to transcode a portion of a source file and watermark effects in Compressor 4 Help.