First: it is best to avoid the use of merged cells entirely. Use "Center Across Selection" instead.
However, the fact the cells are merged should have no effect on running code, assuming you are using the worksheet_selection change event or a properly coded macro to identify the target range.
Perhaps you should post your code / sample workbook so we can take a look.
If cells A1:B1 are merged, this code will still execute and show the userform when the merged cells are selected - notice that only cell A1 is referenced below, but it could also be "A1:B1".
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