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Just got a tuner, need help!!!

So I bought a decent bass and amp about 5 years ago and never really touched it. The other day I decided I would try to pick it up, but knew I would need to tune it. I bought a KORG tuner from Amazon and I am having some difficulties. Every string I play is wrong (ex. E as HC and G as 4E) and I have now spent a couple hours attempting to get it right, however, it seems I can adjust any string to anything other than what I need. Also a few times while trying to get E, the tuner will say it is HC and switch to 3A and I know that none of the other strings are playing. Please help! I am new as I explained and am not sure what I am doing wrong.
 
Warped neck, intonation, and 440 vs 445 would have no bearing on this. A warped neck will still play open strings. Improper intonation... again no problem with opens. 440 vs 445, doesn't make a difference unless you're playing with another instrument (ie, the instrument will be in tune with itself either way).
I would question how the tuner is hooked to the bass and if it is set to the right instrument.
There are lots of korg tuners. Do you have a specific model number that will help identify problems?
 
I am thinking that your problem is as simple as how out of the tune the bass is. The tuner has no idea which string you are playing. It just knows what frequency is going into it. So when you are playing your "E" string and it says it is a "C" then your top string is tuned to "C" and you need to adjust accordingly.

Try Invalid Link Removed to get it in the ballpark if you are new. It will at least let you compare what your string should sound like compared to what your string does sound like. When you get in the ballpark your tuner will be much easier to use.

For example if you get in the ballpark and you play your "E" string and your tuner says "D". Then you simply need to tighten the string up a little bit to "E".

The notes go in alphabetical order. A - B - C - etc.

Sorry if some of the advice I gave is a little insultingly simple. You said you are new and the other posts seem to be questioning the tuner when it sounds like operator error to me. Hope that helped.
 
I was questioning the tuner because I was unfamiliar with the output from the tuner. Knowing what the tuner was I could investigate how the tuners output related to its input. No tuner I have ever had ever had an output like "HC or 4E". I didn't want to jump to any conclusions about operator or tuner without understanding what the tuner output meant.
 
Obeygiant has hit the nail on the head. Slacken the strings a little and keep trying to tune up a little at a time giving the tuner time to settle. Turn the key slowly and if the string feels really stiff slacken it off and repeat the procedure. All tuners behave like this to some degree so. It's just a matter of patience. It will get easier with practice.
Even a bass with appalling intonation will be tunable with an open string note so don't worry about that for now. You could try turning the tone control down on your bass and try playing near the neck or closer to the bridge to see wether that improves the situation. If your tuner is the type that clips onto the head of the bass make sure that its not set to pickup by its built in microphone. If it is the type that you can plug your bass into then make sure that it has a fresh battery and dont rely on it's microphone if your bass isnt plugged in to an amp. Good luck and don't give up.