Frequency matrix is used to store frequencies information for a given base at the given position in some sequence.  There are no 'gaps' in real DNA,  'gaps' are artificial elements used to show correlation of 2+ sequences. Actually adding 'gaps' into sequence you add new information and it is based on the algorithm used to insert them.

Here are the hints for you

1) To remove gaps from an alignment open it with UGENE and use "Edit->Remove Gaps" context menu in alignment editor. Save.

2) If you want to rely on gaps in you alignment - select different algorithm, but not FWM nor PWM. For example HMMMER2/HMMER3 profiles are designed to consider gaps in alignment as important information. Note that in this case the result does really depend on alignment algorithm used.

3) If all you need is to view base frequency statistics for your alignment, open it in Alignment editor and use "Statistics -> Generate grid profile"