How big is your vocon board? 1M or 512K? That is a limiting-factor as to your upgrade path. Current firmware for 1M is R07.71.07/DSP 08.03.05. The last 512K version was R05.60.04/DSP 06.05.02 -- and there have been many bux-fixes and enhancements since then.
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Are you using a PL/DPL? If so, is the transmitting station using a TOC (Turn Off Code) or Reverse Burst?
Example: In my area, CalFire transmitts a PL tone, but they do not use a TOC/Reverse Burst, so I will always get the squelch crash at the end no matter what my squelch settings and having the correct PL entered. Same thing on a couple local 2M machines.
It could also be your moniter settings, if it is set to silent or open squelch.
You might try playing with the channel Mute/UnMute settings. If you are set to AND instead of STD that might cause the radio to not mute until it loses PL AND the received signal goes away. Or maybe it's AND instead of OR - I can't remember exactly, it's very confusing - Read the help for that screen thoroughly, and compare the channel parameters screen from your MTS2000, as the RSS/CPS is nearly identical and the same channel muting parameters apply. Make sure they are set the same...