yeah I'm pretty sure that's what's going on. There is the lengthy unappealing page 2 of the worksheet that does make you factor in multiple jobs and if your total wages from said jobs is over a certain amount. The amount an employer withholds is based on tables generated by the IRS in the wonderful sleep-aid, Publication 15. They calculate the withholding on each paycheck as if you have/will receive that amount each pay period throughout the year.

Two easy options:
1. claim 1 on one job and 0 on the other.
2. figure out about how much you end up owing each year, divide it by the number of pay periods at your main job, and claim 1 with that amount as extra withholding.

One easy but annoying option:
1. make periodic estimated tax payments (e.g. $100 a month)

but yeah ... the system is ... clunky, to put it nicely.