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Sean,
If you add a version - it won't turn up in open issues, unless it has issues assigned to it. Is that your case? If so - does is it just a soap problem? Did you do an import at all? Not my case, no. I did add a few (2) issues to this new version.
This was my procedure: 1) Add a version to the project. Hope that helps. I've confirmed this. From my testing this problem seems to be reproducible after having restored from backup.
As with This was resolved in the 3.6.3 release. The problem was that the managers that the axis servlet were holding onto were stale once an import occurred. We now have a bit of trickery so that we refresh the entire graph held by the axis servlet so we will not run into these "out-of-sync" issues any longer.
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JRA-10272.