Blinking question mark folder icon on startup (but not always!)

I recently obtained a new hard drive (Western Digital 80gb) and installed the Mac OS on a 500 mhz Cube; the DVD drive was not recognized but I removed the jumper on the drive pins rendering the disc a master and finally, the DVD drive was found so that I could perform the OS install. The problem is that if I start up the Cube after a long period of time having been OFF (e.g., 5 hours) there is the blinking question mark folder (Mac OS logo alternates with question mark). After 3-4 minutes, the startup disc is finally located. Now, if I do a cold restart a few minutes later, there is NO problem on startup. My startup issue always occurs after a longer period of time with the Cube having been OFF. There is a new battery installed, permissions are fixed, the drive checks out without problems with disc utility. What could be the problem?

Probably your PRAM battery is gone. This stores information such as your preferred startup disk. I know you said you put in a new battery but have you actually tested it? The computer being off for several hours really, really sounds like a bad battery. Also check the terminals both on the battery and in the machine aren't corroded and it is seated correctly.
[Texas Mac Man's PRAM, battery, PMU tutorial|http://www.geocities.com/texas_macman/pram.html]
[Apple's PRAM reset directions|http://docs.info.apple.com/article.html?artnum=2238]
If you have a digital multimeter you can check the condition of your present battery. It should read at least 3.2V if it is the 3.6V half-AA battery type. Ideally this should be measured while the battery is under load; added recommendation from Hans777:
I have recently found out that an exhausted battery will still indicate >3.6 V with a high internal resistance VM.
Checking incircuit: powercord disconnected press PMU reset button for >about 5 sec before measuring.
Checking outside: load the battery with a 1500 Ohm resistor when measuring.
[Resetting Cuda/PMU on Power Mac G5, Power Mac G4, Power Macintosh G3|http://docs.info.apple.com/article.html?artnum=86760]
Message was edited by: Limnos

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    what's next?

    Did you ever find a solution to your problem? I too have the same problem with a 12" G4 PowerBook DVI that I just bought off eBay. The original owner claims to know nothing about it. Sometimes it boots just fine and sometimes it starts up with the screen that you're describing.
    Here are some things I have done already:
    - Reset the PRAM. (multiple times)
    - Rand Disk Utility from both within the OS and from the rescue CD. Fixed permissions and verified the hard disk. (multiple times)
    - Formatted the hard drive and did a fresh install as well as all available updates from Software Update.
    - Bought a brand new battery, made sure it was fully charged and tried booting both with the AC adapter plugged in and also running soley on battery.
    - Made sure (once it booted) to select OS X as the primary startup disk.
    If it helps, here are some specs on the computer:
    - 12" PowerBook G4 DVI model. 1Ghz, 1.25GB Ram, 40GB HDD.
    I haven't tried resetting the PMU because I can't figure out how to get the keyboard to come off. I suspect a faulty HDD because that's all I can think of at this point. I'm probably gonna have to take it to Apple if you guys don't have any ideas. Just thought I'd check here first.
    2Ghz 15.4" MBP, 1.5Ghz 12" PB, Dual 2Ghz G5 PM   Mac OS X (10.4.6)  

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