INSTRUCTOR AND STUDENT PLTS ABOARD VLJ EXPERIENCE LOSS OF COMS WITH TWR DUE TO AVIONICS IDIOSYNCRASY.

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MY STUDENT AND I WERE FLYING AN ECLIPSE JET DOING PRACTICE APCHS AT ZZZ. WE WERE HOLDING OVER THE ZZZ VOR AND COMMENCED THE VOR RWY 33 APCH WITH THE GOAL OF DOING A CIRCLE APCH TO A MISSED APCH. INBOUND TOWARDS THE VOR THE STUDENT WAS TRYING TO INPUT THE MINIMUM DSCNT ALT VIA THE FMS KEYBOARD. HE HAD INPUTTED IT CORRECTLY SO THAT THE AURAL WARNING WOULD ANNOUNCE; 'APCHING MINIMUMS' AND 'MINIMUMS' BUT WAS TRYING TO SET THE MDA INTO THE ALT SELECT WINDOW SO THE AUTOPLT WOULD LEVEL OFF AT THE INPUTTED MDA. THE CURRENT AVIONICS SUITE IN THE EA50 HAS A FEATURE THAT WHEN THE NAV PAGE IS SELECTED; IT RETURNS TO THE COM PAGE AFTER 30 SECONDS AUTOMATICALLY. AFTER THE STUDENT REALIZED THAT HE DID NOT 'DRIVE' THE MDA UP TO THE ALT PRE-SELECT HE PUSHED THE CONCENTRIC KNOB WHICH WOULD NORMALLY DRIVE THE MINIMUM ALT TO THE ALT PRE-SELECT WINDOW BUT AT THIS TIME THE NAV PAGE HAD RETURNED TO THE COM PAGE. THIS CAUSED THE COM FREQS TO SWITCH OVER WHICH MADE OUR STANDBY FREQ ACTIVE AND WE DID NOT CATCH THIS. AFTER LEVELOFF AT MDA; WE HEARD RADIO CHATTER BUT SOMETHING DIDN'T SEEM RIGHT AND WE THEN CHANGED THE FREQS APPROPRIATELY. AT THIS TIME ZZZ TWR SAID THEY TRIED CALLING US. WE APOLOGIZED; COMPLETED THE APCH AND LEFT ZZZ AIRSPACE. WE WERE GIVEN A NUMBER TO CONTACT TWR. UPON LNDG WE CONTACTED ZZZ TWR AND HE ADVISED US OF THE IMPENDING SITUATION THAT COULD HAVE OCCURRED. WE TOLD HIM WHAT HAPPENED AND HE SAID THIS WAS NOT THE FIRST TIME THIS HAPPENED WITH THE AVIONICS IN THE ECLIPSE JET IN REGARDS TO MISCOM. WHAT WE LEARNED FROM THIS WAS TO ALWAYS VERIFY THE XMISSION FREQ AS PART OF THE SCAN BECAUSE OF THIS 30 SECOND CHANGE OF FREQS THAT IS STANDARD ON THE CURRENT AVIONICS SUITE; AND BE VERY AWARE OF OUR FREQ AFTER THE MINIMUM ALTS ARE SELECTED AND DRIVEN TO THE ALT SELECT WINDOW. THE APPROPRIATE ORGANIZATIONS WITH ECLIPSE AVIATION CORPORATION HAVE ALREADY BEEN NOTIFIED TO BRING AWARENESS TO OPERATORS OF THE ECLIPSE JET.