Do you have any power saving settings on? If so , disable them all.
I also have heard that you can't have the wireless assistant on as well, as that causes connection problems like your experiencing. So turn that off as well.
Also ensure that all connection managers are killed off. This can cause problems as well.
If possible, try the 1.0dev version and see if that fixes the problem.
1. Madwifi-ng known issue: after some time (can be 5 minutes or 50 minutes or more), it doesn't report a packet anymore, you have to unload and reload all modules
2. When Airodump-ng doesn't get a packet from a client/AP anymore, it is removed from the screen after some time (but still shown in text file)
Hopefully, with luck, one of these ideas will fix your problem..