I never heard of loading an EA into EA Studio and it changing the EA into a different version. I always reset EA Studio before using it so maybe try resetting EA Studio before loading an EA into it and maybe this will keep EA Studio from changing the EA into a different version.
If MT5 is set up for Hedging instead of Netting you can see both long and short positions for the same EA. If MT5 is setup for hedging you will need to have your broker change it to Netting. Note, MT4 only does netting so it will only place either a long or a short trade for each EA but not both long and short at the same time.
Alan,