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Its just a problem that Trillian has. When new versions come out, they sometimes conflict with other programs, like Trillian for example. Trillian Pro came out around the time MSN 5.0 was in use so it's expected that conflicts may arise when something changes. The people at Cerulean Studios (who created Trillian) are at work on a new version of Trillian which should solve most of the problems we see now with it (including file transfer issues between Trillian and MSN 6.0). Just be patient.
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