The system has a certain total volume. If somehow air is replacing fluid anywhere in the system, that air being pumped thru the system could cause the reservoir to overflow untill the air is purged. Is it jerking or operating erratically at any point? That is an indication of air
Tell me about this filter? Is it a spin-on cartridge down on the right side of the tractor between gas pedal and hydraulic pump? If so a better term would be a strainer as it is on the suction side of the pump I am guessing...
Also what type fluid are you running in this hydraulic system? Should be AW-32 in most cases unless you are in some temperature extreme environment.
Hydraulic pumps are great at pushing fluid, not so great at sucking fluid. IF that "filter" is as I described, you need to be carefull of the specifications for it. It should probably be a mesh strainer core(#100 mesh) specifically designed for suction side applications. If it is too restrictive, it will cause the pump to cavitate(does damage) and to also pull air in thru any weak spot in the system like the pump O-rings or the O-ring seal on that spin-on cartridge. IF the pump got noisier after the filter change, and/or under load, that is one giveaway that the filter may be wrong...
So what could be happening, upon startup when the fluid is it's coldest/thickest, is that the pump cannot suck it thru the filter, and is drawing in air from somewhere along the line or a cracked pump housing/bad seal(you mentioned an oil leak on the pump?). It is pumping air instead of fluid and that air bubble is pushing all the oil in the pipes hoses and control valve and diverter ahead of it into the reservoir without drawing any fluid out which causes it to overflow untill the system starts to draw from the sump then you are low(minus the fluid you burped). Of course if you operate a control lever while this is happening, air will get cent to that cylinder causing erratic/jumpy operation untill that air is purged thru operation...