The probable causes could be due to Data for CD not transfering during the installation. Here some options you can try,
1. Infected PCs. (Scan PC for virus & malwares)
2. Dirty or bad CD installer. (Use another CD)
3. HDD space for the installation.(Remove some of your data for space allocations)
4. Security Programs running in the background. (Disabled any Security Programs before installations)
5. Too many junk files in your "temp" folder. (Use the CCleaner to clean up your PC and reinstall the program.)
Most probably your PC & external HDD is infected with dangerous objects/files eg. virus, malwares, etc... which resulted your folders & files atributes changed to "hidden".
Do a thorough Virus/Malware scan for the PC & External HDD, to removed the "dangerous object/files"
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