Mylyn defaults to a day having 24 working hours and a week having 7 work days. If your JIRA repository uses different settings, then time tracking information will not show correctly when converted between Mylyn and JIRA.
To fix this, change the time tracking settings in Mylyn in the Additional Settings section of the repository properties (Window -> Show View -> Task Repositories) to match the server configuration. Your JIRA administrator will be able to tell you the correct settings which can be located under Administration -> Time Tracking in the JIRA web interface.
Screenshot: JIRA Web Interface
Screenshot: Mylyn Task Repository Settings