Time Machine Issue

Have you checked Finder > select external HDD >> GET INFO >>> Format yet?

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I presume, it is not using the correct Format, which would be Mac OS Extended (HFS+), thus your OS wants to format the HDD correctly.

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Overview of the four major file systems (called "Formats" in Mac OS X) used on Windows and Mac OS X, compiled by GGJstudios. You can use Disk Utility to format any HDD to your liking.

Any external hard drive will work with PCs or Macs, as long as the connectors are there (Firewire, USB, etc.) It doesn't matter how the drive is formatted out of the box, since you can re-format any way you like. Formatting can be done with the Mac OS X Disk Utility, found in the /Applications/Utilities folder. Here are your formatting options:

HFS+ (Hierarchical File System, a.k.a. Mac OS Extended (Journaled) Don't use case-sensitive)

• Read/Write HFS+ from native Mac OS X
• Required for Time Machine or Carbon Copy Cloner or SuperDuper! backups of Mac OS X system files.
  [*]To Read/Write HFS+ from Windows, Install MacDrive
  [*]To Read HFS+ (but not Write) from Windows, Install HFSExplorer
• Maximum file size: 8EiB
• Maximum volume size: 8EiB
• Mac OS X: Mac OS Extended format (HFS Plus) volume and file limits
• You can use this format if you only use the drive with Mac OS X, or use it for backups of your Mac OS X internal drive, or if you only share it with one Windows PC (with MacDrive installed on the PC)

NTFS (Windows NT File System)

• Read/Write NTFS from native Windows.
• Read only NTFS from native Mac OS X
  [*]To Read/Write/Format NTFS from Mac OS X, here are some alternatives:
  • For Mac OS X 10.4 or later (32 or 64-bit), install Paragon (approx $20) (Best Choice for Lion)
  • For 32-bit Mac OS X, install NTFS-3G for Mac OS X (free) (does not work in 64-bit mode)
  • For 64-bit Snow Leopard, read this: MacFUSE for 64-bit Snow Leopard
  • Some have reported problems using Tuxera (approx $36).
  • Native NTFS support can be enabled in Snow Leopard and Lion, but is not advisable, due to instability.
• AirPort Extreme (802.11n) and Time Capsule do not support NTFS
• Maximum file size: 16 TB
• Maximum volume size: 256TB
• You can use this format if you routinely share a drive with multiple Windows systems.

exFAT (FAT64)

• Supported in Mac OS X only in 10.6.5 or later.
• Not all Windows versions support exFAT. See disadvantages.
• exFAT (Extended File Allocation Table)
• AirPort Extreme (802.11n) and Time Capsule do not support exFAT
• Maximum file size: 16 EiB
• Maximum volume size: 64 ZiB
• You can use this format if it is supported by all computers with which you intend to share the drive. See "disadvantages" for details.

FAT32 (File Allocation Table)

• Read/Write FAT32 from both native Windows and native Mac OS X.
  [*]Maximum file size: 4GB.
• Maximum volume size: 2TB
• You can use this format if you share the drive between Mac OS X and Windows computers and have no files larger than 4GB.

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OP,

As long as your data structure is manageable (meaning that you know where the data for each backup lies and it not a hassle) manual backing up is by no means an unworkable solution.

Naturally you could also get a separate drive for each operating system's backups. So for instance assuming that your use is concentrated on the Mac side and your windows use is sporadic, you could use an external HDD for time machine and manually backup the windows-side data on a USB memory dongle.

RGDS,