External edit (TIFF) and metadata

For some weeks (I guess since I'm using Max OS X Lion or since I'm using LR 3.6) I got a problem with all external edited photos after the external changes are imported into Lightroom.
If I make any changes on metadata (or editing the photo in develop module) after I've edited a photo in an external editor (in this case it is Nik Silver Efex Pro 2) Lightroom can't write metadata anymore.
The original files are DNGs created from Leica M9 DNGs (uncompressed) by Lightroom 3.6 on import and I use TIFF-copies for external editing in SEP2.
To be completely clear, here's my workflow:
import as DNG
basic edits in LR develop module
right-click > edit in > SEP2
use copy with LR-changes: TIFF, 240dpi, ProPhoto RGB, ZIP-compession
convert to black and white in SEP2
save and go back to LR
change metadata or sometimes make some further adjustments in LR develop module
>>>  warning sign on photo (grid view)!
If I then re-import the metadata from the file all changes in Lightroom after the external editing are gone. Saving the metadata again doesn't work and changes nothing.
Does anybody know if that's a bug (in LR, Lion or SEP2) or if I can do anything to prevent that problem in future?

Sorry I should have been clear - I am referring to IPTC metadata.

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