Hi Skibumwa
We came up against this too. My OH left Malaysia when he was 17 but we didn't realise that he needed a police certifcate til just before we were due to submitt our work visa application. We had to change from a 2 yr visa to a 18 month visa which means that we don't get healthcare entitlement.
Anyway, OH was told that if you are in KL you can go to Putrajaya and get the certificate in a day. We were in London so were told it would take 2 months. We considered flying out to Malaysia to get one, and then applying for the permit in Singapore, but OH could do that, I couldn't as I'm British. His certificate is now sitting in Scotland but did take several weeks.
We now need new certificate from London and KL to apply for PR. The timing will be difficult.
I suggest your girlfreind goes to Putrajaya and applys in person. If they make a fuss, she could try telling them she is seperated from her love... And I have to say a few tears may come in useful. They tend to melt the heart.
Alternatively, she could have the option of signing a waver but this wasn't acceptable for OH. I suspect things may be dependant upon who you see on the day.
Good luck. Don't give up hope.
Julie