We are a commercial printer. I've seen pages on many jobs recently where RGB images are converting to CMYK using SWOP profile, but no black sep information is present. The image separates into 3 colors only. When exporting from ID, we suggest leaving color unchanged, since our RIP has always done a great job of converting RGB to CMYK. Has anything changed in CS5 that would cause this?
There has been no changes in Adobe color management since at least CS2. Color management is turned on and is unified throughout the Creative Suite if you're using default settings.
Choose Edit > Color Settings and see if your InDesign settings are Synchronized with the Suite.
If you're outputting directly from InDesign, you might try resetting your InDesign preferences. Perhaps something has gotten screwed up:
When exporting from ID, we suggest leaving color unchanged, since our RIP has always done a great job of converting RGB to CMYK
If the PDF is exported with Output>Color Conversion>No Color Conversion, then any ID RGB objects export unchanged. So in that case any CMYK conversion problems would be happening when you send the PDF with RGB to the RIP—ID isn't making the conversion.