This bug is best and easily explained through pictures, I suggest you take a look at the four pictures at the bottom.
This bug is a bit harder to explain through text, but I'll try my best. If you're directly powering a block, which indirectly powers a repeater, through a powered redstone cross then turn that redstone cross into a redstone dot, then the repeater will unpower itself. No problems there. Then, if you attach another redstone component (such as a repeater or a redstone dust) to the redstone dot on the side opposite the indirectly powered block, then the redstone dot will turn into a redstone line, but it will not update the directly powered block and thus the indirectly powered repeater will remain powered off, even though visually and using block-states the indirectly powered repeater should be powered.
That was a complicated wall of text. What I'm trying to say is, the redstone dot being changed to a redstone line from another component isn't updating properly.
It's really hard to explain through text, so just take a look at the four pictures below.
Step 1:
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[media]Linked issues
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Still having this issue on pre-release 3.
With some testing, it seems that redstone dust in place of the redstone repeater updates the original redstone just fine, but a redstone repeater does not.
Confirmed, affects pre-5

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We're tracking this issue in MC-3703, so this ticket is being resolved and linked as a duplicate.
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It happens to me too when changing the dot to a wire, then reversing it to a cross but it is still powered but does not power the blocks on the side except if I put blocks next to the redstone lamps, then it updates and the lamps are powered, same if I purposely change it to a dot and then to a cross again
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