I don't know either why you'd get different results, but the way to restrict searches to a grammatical category is simple. On the command line, input your search string, place the cursor at the right end of the string (necessary when searching in Hebrew), then type @. This should produce a drop-down list of parts of speech. (If it doesn't, right-click in the command line, and be sure Command Line Morphology Help is selected.) Then just type n for noun, v for verb, etc. If that's all the specificity you want, type * to have all the remaining possible morphology codes (for gender, number, etc.) included in the search; or keep typing codes to get more specific.
There can still be some problems with this. Searching for the root DBR with noun specified as the grammatical category will return both dabar, word, and deber, plague. But it will eliminate all instances of dibber, speak.