The situation now:

Putrajaya :-

1-5 passports -- Drop today and return tomorrow (not confirm will complete, need to wait for them to call after wrote your company name)
>5 passports -- Wait a week (but was told by others that they waited for more than 2 weeks with no answer

Jalan Duta :-

Queue numbers will be distributed to those who queue. Queue start at 7AM, numbers distributed around 8AM, and once reach the end of queue, no more numbers will be given. Troublesome for me since I had to fetch kids to school and wife to work. Especially annoying if they had system down and had to queue again the next day.

Shah Alam :-

Same with Jalan Duta.

I believe this may well be the best answer yet, unfortunately. In the end of the day, its the workers who paid the extra, not employers (although my boss did paid for our employees since we only had few). Our agent want RM100 per passport for the same damn job.

The registration process (as explained to me) was relatively simple. You just need to certify true copy company registration, employer IC, representative IC (if any) and make an appointment with MYEG who will sent man over to collect your thumbprint. Actually I had hoped that they required employer to buy a thumbprint scanner so that worker need to scan their thumb to register for renewal. I believe this would close the loopholes for runaway workers but wont be done as it will provide "additional" income.