I don't have filters but by exporting the filters I have figured out the problem.
The issue is that the filters are saving also your preferences for reputation.
To use an example; you create a staff filter for a Physio. If you create this filter and have 'Realistic appointments - Youth Team' set, you then save the filter it remembers that you have 'Realistic appointments - Youth Team' set. So next time you use the filter you will always have that preference. This means if you have a filter to find a Physio, you have to keep 3 different filters for the same role based on whether you want a First Team, Reserve or Youth Physio.
Same with player search. Say you create a filter it will always remember your 'Interested in' field. If you want to create a filter for a striker, it will remember that you had 'Interested in > Slightly Interested' from when you created the filter. But if you decide to look at players instead that are very interested you have to change the setting after each filter you import.
So, I guess this needs to be in the feature request section?
Filters saved should not be remembering reputation toggles, so you can freely use the same filter for your last selected preference.
Does this make sense?