This may be happening because Project will want to use it’s own ID field, not the one you have created in Excel. This then causes an issue if the IDs are not in synch – I suspect this is your issue. Two ways around this that I can see….
1. Cut and past the info from Excel into MSProject – though the IDs may still be an issue.
2. Get your PMs to start in MSP2010 – and give them training in using Manually Scheduled tasks etc. With 2010 and these features, there really isn’t a reason to use excel anymore….