I had a look to
"<koen> booting improved when enabling the CONFIG_OMAP_MUX, but that kills ehci"
from yesterdays IRC .
Koen: Can you please try to delete the line
OMAP34XX_MUX_MODE6 | OMAP34XX_PIN_OUTPUT)
in file arch/arm/mach-omap2/mux.c and check if ehci is still broken if you enable CONFIG_OMAP_MUX?
Looking to HW manual  at
Figure 34. Host USB Port Design
and uboot pin mux
MUX_VAL(CP(ETK_D10_ES2), (IDIS | PTU | EN | M4)) /*GPIO_24*/
#define CONTROL_PADCONF_ETK_D10_ES2 0x05F0
at Beagle 0x05F0 has to be configured for GPIO and not HSUSB2_TLL as kernel pin mux does.
If this works for you, we have to check which kernel pin mux config is correct for beagle and which causes the boot improvement.