Have you installed any fan made flags?
It sounds like the problem that occurs when you have an image referenced in a config file, but there is no image in the folder with the config file - so the game will try to 'call' the image but fail.
Check the folder \Football Manager 2005\data\graphics\flags for duplicate config.xml files, look in the config file with notepad and check the references for duplicates.
Or you can uninstall/repair Football Manager, backing up any extra files you have added to the game (kits, logos, player pics, balls, skins etc...). Reinstall it apply patch, test game see if flags show, slowly put back added pics/skins etc... test to see if flags disappear if they do, don't use pack affects flags or edit its config file. You can add packs individualy by transfering them to the approiate folders within the FM folders, and changing skins in game should cause FM to reload all graphics, so after adding back one pack, change skin and see if flags start disappearing, repeat until all added or flags disappear.
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