My Rio was doing that and I ended up going back to 1.03 no Hijack then I put on the dev 2.00b11 and the latest Hijack then the problem was gone, but I edited my config.ini so I can't go into aux mode (I don't use aux mode).

[ir_translate]
20DF03.L=Top.L,null ;Long press goto standby
20DF03.T=Player ;If in tuner change to main
20DF03.M=Top.L,null ;If in main goto standby

The code (20DF03) is for the Rio remote source botton.
Hope this helps.