Have you tried going quiet, not making contact to see how she reacts ?
I did try that just before christmas for 3 days, then I got a message from her asking why I'm not talking to her and am I growing tired of her. I just laughed at that coz she can disappear for a week and not say anything.

There are definitely some very remote areas where there is no phone service or Internet. Whereabouts is her home, and where is the 'province'?
I'm not exctly sure. She's from Davao and says its about 4 hours away by bus. I did believe her about the phone reception/no internet thing because when I was there for the first week her parents were away in the province and she said she didnt know when they'd be back because there was no way of contacting them. One day her mum and dad walked in and everybody looked surprised and excited.

This makes it sound as though she is trying to contact you - how does she always manage to pick a time when you're not there?
That's it, almost every day I'm getting the same message - "are you there?" but its usually at a time just before I get up in the morning. Which is kind of annoying as she knows the time difference and when's a good time to catch me. We did speak briefly when she got back, almost a week ago. I had just woken up, we had a little chat and I asked if she could give me 2 mins to freshen up before I put the cam on. She said ok, that she'd go for dinner and try and get back online later. She never did, and its just been these short messages ever since.

Perhaps there is another guy in her life - and that restricts the times when she can get online?
They have 2 PCs there in her house, and she always blames her sisters using them and not letting her get on. Like I said before she knows the best times to catch me, so in my mind there's no excuses.

I guess that if you cannot get to talk to her then the relationship is over.
I actually left her a message earlier saying I haven't got the patience for this anymore, trying to guess what the problem is, and that I'm growing bored with the whole thing. No reply yet.

However, filipinas have a very different attitude to relationships compared with most western women and their reactions may well be very different to anything we're familiar with ... there may be some logical explanation.
That's the only thing that's been holding me back from calling it a day till now, that there maybe some factor involved that I don't understand. If there is somebody else why she's still leaving me messages? I know its not about the visa or the money. I've only sent a three thousand pesos on her birthday (call me stingy if you like lol) so it's not like she'll be wanting to keep me on as a cash cow.

My gut instinct has always been that she's a really good girl and not the sort to cheat and lie, but hey, just 2 weeks together and from the other side of the world you never really know.

I really appreciate all the advice been given here. Thank you all. I'll keep you posted on how things turn out.