The spikes modify the shield's damage, making it a medium weapon that does 1d6 damage. The Bashing enchant then modifies the damage, increasing the damage the shield does as if it were 2 size categories higher. At no point in the entry for Bashing does it say normal damage, base damage, or ANYTHING that would indicate that you use the pre-spikes number.
The only time effects do not stack is when they are from the same type of bonus. Bashing is a magic bonus, while spikes area mundane bonus. By the rules of the system, they stack. Otherwise, no bonuses would ever stack.
