From mid-March until mid-June IRS offices in most locations were closed, with employees working from home. As such, no one was available to open mail and scan documents in. While 3 weeks is normal when offices are closed, 3 months right now is not cause for concern.
It is not known how long it may take for returns mailed in (amended and standard) to be scanned in for processing, but primary returns are taking priority over amended. I can only guess, but I would expect a few more months before the return is logged based on the volume of mail the IRS still needs to open.