It appears that installing houselinc creates and registers an instance of SDM3.exe. When you install the device manager by itself, then it is located under common files as you describe. So, indeed, your main machine has two instances installed.
For your main machine to work reliably, it sounds like the following steps should produce a satisfactory result:
1) First try to uninstall just the device manager from Add/Remove- this may work by itself…
2) Continue cleaning out the main machine of houselinc and the applications / utilities. Do NOT install a separate SDM, use the one the comes with houselinc.
3) Install houselinc first. Then you can install the simplehomenet applications as required.
Let us know if this works for you.