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1. Brush tool with not paint opaquely (takes 4-6 stokes to layer on).
2. Healing brush often just stays black and will not heal.
3. Messages saying no pixels can be selected ... edges will not show
ALL this happens even if there are no layers needing to be flattened
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Have you tried resetting your Photoshop Tools, Photoshop Preferences and check all tool options settings are normal blending 100% opacity and Fill ans set sample this layer and below.
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Your brush tool is likly set to transparent. Look at the top of the screen in the options bar. As for your healing brush and selection edges - I suspect it's a graphics card issue. I've been having similar problems. To get the screen to refresh, I hold down the space bar and just move my screen slightly with the hand tool. The tools are working, you just can't see them.
If these suggestions don't fix your problems, please post a screenshot that includes the options bar and layers - so your whole screen.