DK,
Your thought of checking the clock tree got us to review clock related items - thanks. I want to post what we finally did to fix these USB issues so that someone else may benefit.
I fixed the problems with USB for both u-boot and linux. The short version of the story is that I needed to set the #define V_OSCK to the oscillator value we are using (25 MHz) in uboot’s include/configs/am335x_evm.h file. It had been set to the eval board value (24 MHz). We are using the AM335X SDK 05.06 eval board code as a template.
When you look at uboot's /arc/arm/include/asm/arch-am33xx/clocks_am33xx.h, you can see that the USB Phy clock is derived directly from V_OSCK. So I can see why we experienced USB problems within u-boot.
But it looks to me like linux gets the system oscillator value by reading the 2 assigned sysboot pins, then adjusts all the clock-related fields dynamically at startup (including setting the peripheral PLL register values, needed to generate the USB Phy clock). We did have these pins set correctly for 25 MHz. And at linux startup the console log showed a sys clock of 25 MHz.
I am surprised that changing V_OSCK value in u-boot DID fix our linux USB problem, but also am glad that this issue is now fixed.