I have a PowerShot A540 and a Canon Battery Charger (CB-4AH). The only batteries I've used with the camera and charger are the ones that came with the charger. Those batteries are no longer holding a charge as they should. Which Canon batteries can I get now to safely recharge in the charger I already have?

Is there any indicator lights on ? Is there a poor connection between charger and battery ? Is there signs of corrosion or damage to contacts ?

If you're using the supplied CB-2LX battery charger, then yes. If you're using another battery charger, please check its specifications.

The A3100 comes with a separate battery charger. The camera does not charge with a USB cord.

Technically, the camera doesn't need charging. As for the battery, the camera does not include any charging circuitry. You need to use the supplied CB-2LY charger. If you need a replacement, you can order one from Canon at
http://www.usa.canon.com/cusa/support/consumer/digital_cameras/powershot_sd_series/powershot_sd1200_is#SuppliesAndAccessories

Open camera battery cover check contacts if it oxidize rub it with screw driver and clean it.your problem will solve

I´ve got the same issue. If you use the batteries that were in A540 in another camera, does it still work?

It is not your charger. It is your battery.

Some of The Canon Powershot A530 and A540 cameras are subject to an advisory recall. Seems that a small spring on the battery compartment door can short out the batteries. Suspect this of yours, in that you mention that your batteries aren't lasting long. If your camera is on the list, Canon should fix this for you for free, including free shipping both ways. This is regardless of your camera's warranty status. Please check this link for more info.
　

Your specific manual is here.

You can find Sanyo UK owner's manuals here

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Check your batteries. Your batteries may not be fully charged. One reason may be that you are charging batteries on a different AC Voltage supply, than what the charger is meant for; eg, charger expects 240 volts and you are charging with 110 volts.