Correct me if I am wrong, but it sounds as if the program you are running uses multiple e-mail accounts, and some files are owned by one account, the rest are owned by the other account.
Being unsure of the details of the program, and it's configuration options... it is writing the files to your home directory owned by your true user account.
The simplest fix I can think of is to find the group that it's assigning these files to, and then make the files writable by the group, or by all users if they are not owned by the same group.
You can verify the group by using the ls: -ld <filename>
For instance, on my machine, one of my directories returns the following:
drwxr-xr-x 2 root root 4096 2008-06-06 23:48 bin
In this instance, the first root is the user, and the 2nd root is the group.
As the first response mentioned, you could change this with the chown command:
chown username:group <filename>
and use the -R flag if you wish to make it recursive.
To make the files writable by all users of the owner, the group, but not writable by anyone else, you can run:
chmod 770 <filename>
using the -r flag to make it recursive.
To make it writable by everyone, it would be:
chmod 777 <filename>