Once again, I had experienced something similar on VWs.
The cam lobes do not match exactly, perfectly. Some are more advanced in relation to the normal cam, some are retarded. This is where it gets tricky and you have to split hairs as far as timing the cam. Only experimenting will be your guide here.
On an aside: I had tried this on my motorcycle as this is a common mod on the SV650. The same issues crop up but are a little easier to sort out by mixing and matching drive gears. We had tried this on a Bandit 400 but there were large, very detrimental differences:
-Cam profile was asymmetric: there was more profile ground into the lobes that were specific to the application, not just a normal lobe.
-Greater lift, shorter valve: even if you were able to time them and get them running, the higher lift in the intake position was enough to cause the retainer to contact the valve stem seal. This was exacerbated by high revs: smoke show on decel and cramped quarters to replace them.
-Valve clearances: thankfully the Bandit 400 uses adjustable rockers. We set lash to the exhaust cam spec on the intake side.
The reason these mods even happened: these are a cheat in any production class vehicle. Since the vehicle came with this cam standard, it is generally "allowed" by the rules of whatever organization you are with. If you get broken down in tech, the ex cam has all the factory stampings and obviously no sign of regrind/reweld.
Now that you know the certain caveats, now you know why people just go with a tried and true camshaft selection. I wasted a lot of time on the VW experiment (which was successful) and on the Bandit experiment (which was terribly unsuccessful, costing me a motor at one point).