My boss regularly schedules meetings that we are required to attend at the oddest hours. We are informed that if we are late or do not show, we will be penalized or charged $5.00 per minute we are late. Legally, can he charge us or withhold $50 from our pay if we are ten minutes late?

Also, my employer regularly does not pay all the wages that are due. My check is usually anywhere from 30min to two hours short short. The boss never has a reason for this and it has gotten to the point where it is more trouble to try to fight for that time than it is worth. What are the laws requiring them to pay us for every hour, and every minute, that we work.

Your pay cannot be decreased as a "fine" or "penalty". It's inherent in the regulations.
http://www.dol.gov/dol/allcfr/ESA/Title_29/Part_785/29CFR785.7.htm

You don't have to be made for every "minute" worked; in/out times CAN be rounded to the nearest quarter-hour, as long as it is done consistently no matter to whose advantage the rounding accrues.

However, if "mistakes" in pay occur, the employer must make them right.

If you have not been paid for all hours worked (within the applicable rounding guidelines), file a claim with the state Dept. of Labor.