Can you upload a model? It's very difficult to provide incite into your problem (short of asking you to make sure the components aren't excluded from the BOM, suppressed, etc.) IF you can provide an example I'll gladly look it over and figure out what might be wrong.
Here is a quick example.
I have a Plate configured 2 ft or 3 ft with holes spaced 2inches apart.
With these I created assemblies “Example Two Feet” and “Example Three Feet”.
I patterned dowels using the pattern in the part to generate the correct number of dowels. The table however, displays 12 dowels in each assembly where as it should show 18 dowels in assembly “Example Three Feet”. I hope this makes sense.
Example.zip 335.2 KB
Not sure what's going on with your system... If I start with a fresh launch of SW and open your Example.slddrw, the BOM shows 12 in both columns for an instant, but very quickly updates to 18 in the Example Three Ft column without any intervention from me. What happens if you open the assembly and switch configs?
Edit: I'm running SW18 sp 3.0