1. With your scanner tuned to 144.390 MHz you are indeed hearing your APRS transmission due to the proximity of your scanner to your transmitter. That does not mean your packets are always reaching a digipeater and or an Igate, if the digipeater is not passing the packets to the Internet directly.
2. Your APRS packets could be reaching the Digipeater or an Igate, but so may someone else at the same time and their signal is stronger. Thus, your packets are quashed.
Improving your antenna will help, but passing your packet every 90 seconds may not be helpful to the overall APRS RF network in your area. For example, I use APRS in my vehicle and when it is not moving the beacon only transmits once and hour, if it is even turned on at all. Some operators have their packets transmitting too much. Seriously consider how often you need to send a packet and who would even need to see it transmitted so often.
I am unsure if that radio has DCD Sense. When turned on if the radio "senses" a transmission from another radio, it will wait to send your packet at the timing you indicate, or it may default to a timing, or your radio may not have that feature. If it does, you should turn it on. I think I set mine to 200 or 300 ms. I forget and could be wrong. Again, DCD Sense is 300 ms sending the actual packets should be no where near that frequent. Still, depending on your use you may need it to transmit more often for a short period of time. Some operators use an entirely different frequency and setup their own Digipeater and or IGate for that alternate frequency. This takes the load off of the main freq when experimenting or whatever.
Have fun!