Different machines can have clients with the same machine id (1,2,3 etc), but the clients on one machine must have different machine ids.
From
F@H FAQ - Is there anything special I should do to run on a cluster?
The main aspect to consider is to make sure that the CPUID for each machine is unique. To help fight from having duplicate IDs, the Windows versions (v3 and later) keep their IDs in the registry and the Linux version (v3.11 and later) keep it in a special file MachineDependent.dat.
Ways to avoid duplicating IDs:
1 If you install each client individually, then it's impossible for there to be problem with a duplicate ID.
2 If you use the recent Windows version and have single processor machines, then you should also be fine (for duals, see the above).
3 For a Linux cluster, make sure that if you copy the directory, you DO NOT copy the MachineDependent.dat file. This file will be auto generated by the client to get a new ID.
A Mod will have to check how many duplicate WUs you've been credited for, but it sounds like you're not doing that anymore.