Times in v2 were stored relative to the server's time zone. If that changed (eg: due to daylight savings or other reason) your playlist times would be affected as well. In v3 the times are stored relative to GMT and therefore are not susceptible to this issue.
In fact, the entire playlist timing system has been completely rewritten from v2 to v3, so if I didn't know better I'd say there was absolutely no way you could possibly be seeing such an issue from v2 manifest in v3. If you can demonstrate that this is indeed happening, though, please open a ticket with the helpdesk.