I also have a Dunco enlarger, although with the combined Multigrade/color filter module. But it's difficult to say what the problem is since you are saying that you have problems both when using the built in color filters and the Ilford Multigrade filters.
Are you sure that the filters lift in and out of the light path as they should? You can check this by taking the top cover off. The filter module can also easily be taken out the head, that might make it easier to identify problems.
What kind of Multigrade filters have you tried? Are they old?