(disreguard the question about internal/external calls.. you mentioned its internal)
Is this only on 5240 sets, or is that just the only phone you use?
And I'm guessing this only happens sometimes? Otherwise you're running for most of the year with not being able to use phones?
Is this going on for internal calls only or both internal and external? Internal only would imply problems between phones, and external would be indicate problems between the phone and the MCD.
Since you are running 4x Mxe IIIs because of needing more memory to get to ver 10 (aka 4.2), I'm guessing you have alot of phones (compared to us; we are running 4x MXe-II, but on ver 11 (5.0), and around 550 phones.
If you're not seeing a reply to some ARP packets, that could be an issue. Not sure if its with the phone or what, but you mention that the phones are on a seperate VLAN. How many phones, and how many voice vlans do you have? We have about 400 phones on one VLAN, and I'm thinking of cutting that back drastically, as we have tons of problems with all the phones hitting the TFTP server at once, and seperate vlans & DHCP scopes will allow us to spread the load out better, and greatly reduce the broadcasts per vlan.
Also, I'm a network guy alot more than a phone guy. Your voice network would have to be absolutely flooded and/or dropping packets for a phone to not respond to an ARP request. How often can you reproduce this problem? Do you ever have this issue with two phones on the same network switch?