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I am using the APIC timer for my scheduler so that when the timer gets on a specified time it will call my scheduler through interrupt.. Suppose a user process calls a system code which will disable interrupts...what will happen if the timer fired before interrupts are enabled..will the scheduler still be serviced after the interrupts are enabled?

Yes - the APIC is responsible for queuing interrupts so that as soon as IF is enabled, the CPU will trap and take that exception.

You won't "lose" any IRQs unless multiple interrupt requests come from the same device before the first is taken. Then, only one will be delivered to the processor.