Some years ago I was the author of APRS Messenger.
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It's main feature was to send APRS beacons and messages over PSK, GMSK and MFSK modes on HF.
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One feature I added to it was a timer to delay the beacon sent to the APRS-IS by 10 seconds so that the RF sent beacon heard by an igate would be sent to the APRS-IS first.
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This worked really well
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You could view the raw packet data on APRS.FI and see all the stations who heard your beacons and if it was a direct APRS-IS beacon from your station it meant that no igate had heard that beacon.
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If you are in contact with the author of Pinpoint maybe you could ask him to add it as an option?
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It would be an idea to time how long it takes to send a typical VARA APRS beacon first to get the right timing between RF and APRS-IS beacons.
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10 seconds was OK for MFSK-16 beacons but VARA may be slower.
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Regards,
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Chris GM4HYG