I had that problem to on a V5/V6, i dunno 20 installs now, the first install i did was the same as you say: tray comes out, dussent close, at my V5/V6 the problem even was that there was no sound or display, the problem is the connection piont 9 on a mini Apple Pro, please make sue you did this on on the correct side, if you didn't, your honey will not close the disc tray!!
Piont 9: www.apple-chip.com
Xbox: 100 Euro (X-ecuter 2 Pro)
PS2: 100 Euro (Mini Apple Pro)