Answer supplied by Katrina Exter:

All PACS maps are differential maps. In other words, the absolute level is arbitrary as the dominating source in the background is thermal emission from the telescope mirror. The map-making algorithm simply subtracts the background when making the map. This means that negative values are just as valid as positive ones for the background. Hence, negative background values are to be expected and are no issue when calculating photometry and should be used in the same way that the positive values are.

This is addressed in more detail in the PACS Photometer Quick Start Guide (section, “Science readiness of the photometry products”).

You can find more about the background and its effect on PACS photometry in the Herschel Science Centre short videotutorials on:

Starting with PACS photometry - https://www.youtube.com/watch?v=yLHLA5Jjtiw

And

DealingWithPointSources_phot - https://www.youtube.com/watch?v=R5S8VnfbNEI