I think that's the problem. The visa run companies pay certain people under the table and when you go alone no payment goes under the table,... then you're fakked.
I'm not talking about an emergency travel document. I'm talking about a whole new passport. My Embassy (Belgium) issues new passports within 15 days normal procedure for about 80 EURO but you can ask for an emergency 24 hrs and pay 220 EURO. I'm sure other countries also do this.
Why don't you go to your Embassy and get a new passport? If it is urgent you can apply for urgent issue within 24 hours. Most countries supply this for their citizens at an extra fee.