Please would you start a thread on the dm Server tooling forum in relation to the STS/dm Server tools problems you are seeing. It may be that you are not running the latest levels.
As for the resolution problem: it looks odd. Were there any more diagnostics to indicate what the constraint conflict was? If not, please could you reduce the problem to a small set of bundles and, if you haven't figured out what's wrong during that process, raise a JIRA with steps to reproduce and attach your binary application bundles and list all the dependencies you have placed in the repository so we can look into it.