I wouldn't worry just yet. It's a low power transmitter and it could just be a signal strength issue with a lack of digipeaters and making it to an iGate.
My APRS radio in the truck is running at 4 watts and even with a good external antenna some days I'll get dozens of points show up on APRSIS and others the same trip might get a handful. Same radio, antenna, GPS receiver, TNC and Smart Beacon parameters. Different environmental conditions, different combination of interference, different cars in traffic, different timing with other stations (e.g. lots of collisions both on RF and on the Internet gateway with other APRS packets).
Do you have access to a power meter? If the LEDs are indicating proper operation and everything seems normal just verify on TX it's radiating what you expect. Or if not set the beacon interval to a fixed 120 seconds and let it sit in a place you know an iGate can hear you. Time it for 20 minutes and just see. That's all you can really do. Seems like moving will introduce too many variables to conclude anything.
BTW, I wouldn't do less than 2 minute fixed intervals because some gateways and digipeaters will prioritize and if you beacon too frequently you might get ignored in a packet stack up. There's some intelligence at work with the digipeating and path selection, the way you and subsequent repeaters configure the RELAY, TRACE and WIDEn-N parameters dictates the hops your packet will make and not every TNC will operate identically given the same set of variables.
