Block 4 of 1099-R form has $10,864.34 in federal taxes, but only $5,432 is reflected as tax on early distributions. Why isn't all of my taxes withheld being reflected?

Assuming that box 1 is about $54,320, then $5,432 would be the 10% penalty for an early distribution reported on the 1040 line 59 and the total withholding (20% of $54,320) would be on line 64.  You will probably be under withheld if only 20% was withheld and you are in a higher tax bracket.

The box 4 (or box 12 state) withholding will be added to all other withholding, such as W-2 withholding, and be shown on line 64 on the 1040 form to offset your overall tax liability. If you are not 59 1/2 or older then there will be an additional 10% early withdrawal penalty that goes on line 59 (from the 5329 form that calculated the penalty).