I saw this happen in a recent model - again, it's intermittent. I was able to fix it by defining a calculated field based on the lookup field. Monarch seemed to be happier making filters and summaries from this copy. If the field you fetch from the external source is called , define either just as , or if(isnull(=1;0;[ExcelField]) in case you want to clean up null values at the same time, and then filters and summaries based on should work fine.
Hope this helps,