I have more information about this issue. I've come to the conclusion that u-boot is broken for iMX28 designs that implement section 4.1.2.1 of AN4199 (see my first post for more info). If I apply the previously mentioned patch to the Freescale bootlet code I see a solid 1V8 rail on my DDR for instance, u-boot does not properly initialize the rail voltages in this configuration. Here's an oscope screen shot of the 1V8 when u-boot initializes the power supply...

I've modified u-boot/arch/arm/cpu/arm926ejs/mxs/spl_power_init.c to force the iMX28 to use the 5V supply like the following but no luck (removed battery check and battery brown out initialization).
static void mxs_power_configure_power_source(void){
struct mxs_power_regs *power_regs =
(struct mxs_power_regs *)MXS_POWER_BASE;
struct mxs_lradc_regs *lradc_regs =
(struct mxs_lradc_regs *)MXS_LRADC_BASE;
mxs_src_power_init();
/* 5V source detected, bad battery detected. */
writel(LRADC_CONVERSION_AUTOMATIC,
&lradc_regs->hw_lradc_conversion_clr);
clrbits_le32(&power_regs->hw_power_battmonitor,
POWER_BATTMONITOR_BATT_VAL_MASK);
mxs_5v_boot();
mxs_power_clock2pll();
mxs_switch_vddd_to_dcdc_source();
}
If anyone has any suggestions as to how to fix this issue I'd be happy to try them.