Hi sonycman,
probably it's already too late to respond to you (just noticed this forum exist), but I will do it anyway just in case somebody else has the same problem.
The schematic has CX3225CA25000D0HSSCC (25MHz) on main xtal input and esc-.327-9-34B-C-TR (32.768kHz) on aux xtal input.
So I started Libero 11.8 SP3 and I can use CCC and use Reference Clock -> Oscillators -> 25/50MHz Oscillator which then gets turned into 50MHz which then with CCC can be generating 71MHz (which then can be 142MHz for M3 clock and 71MHz for the busses/memories).
When I use Reference Clock -> Oscillators -> Crystal Oscillator and I can type free range frequency, that is limited to 20MHz. But for 25 or 50MHz oscillators, there is separate dropbox entry which I tested and works for me.
TL;DR; Probably you are using a wrong entry in the menu as there is a dedicated 25/50Mhz option (which I synthesized and works for me).