Indesign CS5 converting spot EPS or AI files to process

I have two EPS files placed in my cover layout that are being changed to CMYK. They are using a spot colour in the EPS file but they don't show as spot in Indesign. The separations don't list them. It's hard to say if this is a problem with Illustrator or Indesign, but it's a huge problem. Saving as AI doesn't help - same thing.

it seems to me that it's a bad idea to completely override a user's colour plate simply because of similar naming. If it's not a bug, it should at least warn you very obviously that your spot colours are being overridden by an end user. At the very least, it should be flagged by Preflighting. When you work with templates that are coming from other users or companies like this, it's not clear what's been converted, since you can have something marked as a spot but not be a pantone. You're assuming that the user has controlled every stage of a document workflow, which often isn't the case.
This is really bad to leave this as is. Like I said, if I hadn't scanned our plates on pre-press, I'd have a very angry Bell Canada as a client (not for much longer), who likely wouldn't want to pay full rate.

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