I think i see what you mean. I set up a Query Data that retrieves values from a uniqueidentifier column in a SQL table. When I run over the results with For Each Value and track tokens, the value was retrived correctly. However, if i try to use the current value in another activity, the token is not there in the tokens menu:

Does that sound like what you're seeing?
If I open the token dialog, the token is listed.

When I picked it from that list while setting up a second Query Data activity, the editbox underlined it as invalid. I clicked OK and ignored the underlining and it works fine at runtime. Other activities don't seem to have this same issue.
So it looks to me like it's a UI bug at this point, but the token is available and the value is passed around correctly when the workflow runs.