It sounds like your account is associated with user mode. As such any clients you install with that account, or client machines you log into with that account, will be changed to User Mode. User Mode essentially assigns the clients' groups and policies based on the user account that is logged in, as opposed to Computer Mode which assigns specific computers to groups.
Most likely what is occuring is the package itself, as mentioned above, is installing machines into User Mode or because all of the User Mode clients are associated with your account name they are getting converted to User Mode upon registration with the SEPM console.
We have a utility that will assist you with converting all of these clients to Computer Mode. You could then move them to the correct groups. I would recommend to call into support and open a case. A technician can provide you with the utility if you desire.
An alternative option would be to manually select each User Mode client, right click on the client, and select Switch to Computer Mode. Once they have been converted to the desired mode you can right click and move the clients to the desired groups.