Setup:
AAI Programmable Structures 0.5.16
AAI Signals 0.4.2
AAI Zones 0.4.3
YARM - Resource Monitor 0.8.18

Place Scanner BP and provide it with power by any means. Using zone Planner mark some resource, ex. stone with configured zone marker (see constant combinator in BP). Scanner should replace your scan marker with matching resource marker, for stone - white X (perfectly works without YARM). But it will not, because stone signal received from
tile scanner does not match available stone signal (can be noticed using step by step debugging in editor mode).

Scanner Blueprint:

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fVPbt2Ry685tbXHLK+9mvbT/vhNADhdC0drZL6ANySQmDeMxjcxUj3hu108VGrmIOmQ8IZA2oxXCOMquZblGEtkmeEdL
TV2KMF8g2BqjrV4gRGOAWiuRZmbQRD6EHGFeMnuyqY0AKGRoAyCMuTXVOiB9uYaac3MTIC2RP6oo9HRxWA+8zaaE
bd3hzSyEfTGgJcfviSDxfo7+dRfqZ+4A/3A+iYNAR/uCHcgvV1BPXeBEqdpRn9yVi+wCBdkMOcHT56wKhRi48eMDqyx0P
Y1z7PFBWDHTT4Wx1UW7Cge03hWYshtXWKvvmtZDlO2DZh8qqGOmloMKCPzSmvj4EuzO6HofUKRpELN+HZjJXreNA
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DCZMfhHGTsuythxAmNGF2Y48koM13253Zmk4cNbhdF6TGrPU1+70vpRY52Jt5ShG4bb+vITRGhdG5qWTThv2RwdAxv
TGHjTbJ7q7oz0Z2RaOv5Xjp5B3HpIwEBlcYZL/9ipwnWm0vmvt+7Np8ZyOHUQd+HF/bRzwXDj7tjymzmawf3/UdqRe7w
TvdbKJ6u7p8UX/7BZoEApltqA74i/fDn/SCe3D1Ld1rzQc2AYwdD3/ab5DfCKaPg=

same
EDIT: Works in 1.1

Same problem, only the newest version though, it always worked fine when i played on factorio 16.51

I'm unsure if the problem was ever resolved, but this problem is still a thing.
YARM adds a second version of each ore, which is unable to be found in the circuit channel selector. This means that for certain mods that have us check the tile against a circuit channel (such as scanning the floor and matching it against "Iron Ore"), the new hidden ores are a big problem.

This could be fixed by either not adding new resource types, or adding the new ore to the circuit item channel list.

Please fix it

It worked for me when i disabled the "Entities" option in the Tile Scanner. With it there was a different signal, when disabled it outputs the "correct" ore signal: https://imgur.com/a/al57W87

@ghundae THANK YOU THANK YOU THANK YOU THANK YOU

Sorry for the late response, I'm years behind!

What YARM creates are some fake items that create ore entities when placed (if you could get one), which allows the selection tool to show them as a summary of how many ore entities you're dragging over. This is a nice little convenience but not actually necessary in any way, so the obviously correct solution would have been to make it a mod setting, which I have added in a patch for the next release. Defaults to off and the description has a hint that it plays badly with AAI Programmable Structures (and possibly also others), but I like it sometimes.