| Not quite sure what you mean about the Alarm. I have a Veto fitted to my 748 and that will only disable the tilt switch from Normal mode. You have to switch the ignition on and press the button to enter service mode. Is that what you mean isn't happening.
Anyhow, on the subject of your battery. My alarm will Eat the battery in day and so did the Motoguard I had fitted on my ZX9R and so did the immobilizer I had on my Golf GTI. I would guess from my experience that most after market Alarm/Immobilizer eat batteries.
What I've done, instead of using an Oximizer or similar. I've wired a nice sexy little power supply socket to the dash on my bike with a diode and fuse in circuit (so you can't short the bikes electric’s). I then converted a small plug in power supply with a Regulator chip to hold the voltage at 13.8v. Every time I park the bike up I plug in. Much more convenient and won't overcharge the battery. Gone off at a a tangent really! Not sure what's causing you starting probs but maybe this will help you preserve you new battery  | 
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