[M1] Issues after dieing or resetting

[Flower]

I have an urging problem!
After samus dies, or you reset via start, up+a on the second controller, there are certain issues.
The sidehoppers jump higher.
Samus' palette changes.
And the biggest problem: the max. amount of missiles and etanks change. (mostly less missiles and more etanks. - the missing missiles are not in the game any more so that's no "generate password tracking data" problem.)

I really don't know what's going wrong! And foremost i don't know what to do. Maybe when resetting there is some bit set wrong or stuff like that.

Help please!
@snarfblam do you have tackled this issue yet?
@Grimlock did you have this problem with Rogue Dawn and could you solve it?