May be a problem with the alarm rather than the immobiliser. Try re-tuning the key in with one of the spares. I think the proceedure may be in the handbook, else have you tried clubpolo.co.uk?
If they suffer the same issues as the Leon's then its either your Keys that need replacing (which i doubt as its highly unlikely that both will go at the same time), or key reader needs changing or the dashpod is on its way out as it was in my case.
unfortunately its trial and error, you are probably best speaking to a VW specialist, go for the cheapest option then work your way up, if you like i can give you the name of a guy who is excellent with SEAT's he may well have VW knowledge too, he was the one who diagnosed mine, dealers were no use whatsoever! the difference between my fault and yours is my car would start up then cut out after about a second and the immobiliser light would flash constantly
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