Nope, should not be a problem!
But move your modem somewhere else....
There might be 4 possibilities?? why your modem sharing IRQ w/ your AGP card.
1. you installed your modem on PCI-1
2. you installed your modem on PCI-6 (some mobo does share PCI-6 w/ AGP-ISA bridge)
3. you are using AMR modem.
4. you are on Win2k and ACPI is on.
Eitherway, you should be fine.......have it on PCI 2.
or PCI 3 (might share IRQ w/ your onboard AC'97)
or PCI 4~PCI 5 (sharing IRQ w/ your USB devices)