@blue-spirit
I only have Classic and Gamecube controllers so i will test with those to see if they have the same issue. I will get back with results soon...
Edit:
Ok, i have tested SS mGBA with both Classic and GameCube controllers and cannot reproduce your issue. D-Pad and Analog are working correctly using both controllers for me.
Which mGBA dol are you using, 0.9.2 or 0.11-dev? Just asking so i know we are testing the same core.
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Load SS-mGBA core then load any game. When game launches press home button to enter menu, now select Settings/Input...
User 1 Device Type = RetroPad
User 1 Analog To Digital = Left Analog
Now scroll way down to and set...
User 1 B button (down) = 46
User 1 Y button (left) = 45
User 1 Select button = 48
User 1 Start button = 47
User 1 Up D-pad = 50
User 1 Down D-pad = 51
User 1 Left D-pad = 52
User 1 Right D-pad = 53
User 1 A button (right) = 46
User 1 X button (top) = 46
User 1 L button (shoulder) = 44
User 1 A button (shoulder) = 43
Try the above input settings and see if it fixes your issue please.