Well that doesn't make any sense to me.
SMF handles sessions on RMRK.net, including for the pokemon system which is tied into it. I just put the last encountered pokemon in your SMF session. The key for the pokemon in your session is always the same, it's either set (because you have no pokemon in your session) or it's overwritten from an old encounter that wasn't attempted with a capture. If your session refreshes/expires then the pokemon is lost as the old session data both doesn't exist any more and wouldn't correspond to you any more anyway.
I can't reproduce the issue even after testing it to hell and back encountering / capturing hundreds on my local RMRK mirror, I can only make it happen when encountering multiple pokemon simultaneously in multiple tabs / windows, which is the normal newest encounter capturing behaviour. It's only possible to have one encounter per page too. If a post triggers an encounter, all subsequent posts are prevented from doing so.
I dunno, and I wouldn't know where to start about debugging it. Put up with it, I guess :|