I wonder if it has to do with the $PRPSHEET being mapped to the model and assembly. $PRPSHEET pertains to the drawing. Because is it is being mapped to the models they could be overwriting the drawing property with a blank value.
I think Bill is correct. To use the $PRPSHEET attribute mapping as intended, it should only contain the slddrw extension, while the CustomProperty block should contain all three SLD (sldprt, sldasm and slddrw) file extensions. I'm not 100% that this would fix the issue you are experiencing, but do believe it is related.
Did you try saving the drawing before checking it in? Check out this SPR:
SPR 482621 Part or Assembly custom properties copied to Drawing via $PRPSHEET variable mapping should not require a resave of drawing to work