Error checking time depends on the size of the partition being checked and how much data is on it, so it makes no difference whether it's FAT or NTFS in respect of how long it will take.
However, that aside, NTFS is preferable because it's more robust than FAT, providing a more stable system less prone to crashing --- especially if the new disk you've bought, or a partition on it, is to hold the operating system.
If you still insist on using FAT32, this from Microsoft:
"You cannot format a volume larger than 32 gigabytes (GB) in size using the FAT32 file system during the Windows XP installation process. Windows XP can mount and support FAT32 volumes larger than 32 GB (subject to the other limits), but you cannot create a FAT32 volume larger than 32 GB by using the Format tool during Setup. If you need to format a volume that is larger than 32 GB, use the NTFS file system to format it. Another option is to start from a Microsoft Windows 98 or Microsoft Windows Millennium Edition (Me) Startup disk and use the Format tool included on the disk."
http://support.microsoft.com/kb/314463
Linear Mode
