I assume you are using PBP's "On Interrupt..." rather than your own Assembler Interrupt.

In this case the interrupt is not serviced until AFTER the current Basic command has finished executing... this means that if you have a ONE SECOND delay in the form of...

Pause 1000

then the interrupt will not occur until AFTER the Pause 1000 has completed. That means at worst-case there could be a 1 Second delay before you jump into your ISR.

How can you improve on this? Simply break your pause up into smaller segments...

For ByteCounter=1 to 100
Pause 10
Next ByteCounter

Here the overall timing is still 1 Second, but the interrupt will be serviced after 10mS worst-case instead. You can use Pause 1 instead for an even faster Interrupt Service, however, when you get down to 1mS instructions, and if timing is critical to you, the extra processing for your Counter Code will start having an impact to your timing... example...

For WordCounter=1 to 1000
Pause 1
Next WordCounter

...here you may find that you have not got exactly 1 Second, but 1.05 Seconds or thereabouts (the actual figure depends on many factors). Then instead of using Pause 1, use PauseUS instead, and adjust the value to compensate to get as close to your overall ideal 1 Second as possible... eg...

For WordCounter=1 to 1000
PauseUS 995
Next WordCounter

Melanie