[Bug] ymdk_np21 works unreliably after update

I used some older version of QMK for probably a year or so and decided to upgrade recently.
Everything worked without issues before update but then suddenly I have multiple problems with QMK.

I didn't pay attention to which version was working because I didn't think I could get malfunctioning keyboard after update.

Describe the Bug

1. When I press any configured key (e.g. C(KC_F13), C(KC_V) and both tapdance actions for ACTION_TAP_DANCE_DOUBLE(S(KC_F16), C(S(KC_F16))) are ones that I use often) it can sometimes be ignore.
   I don't see any correlation with time between keypresses in any case.
2. Sometimes I get multiple events fired. For example. one of the keys is A(KC_F4) and it could just happily wipe out all the windows I have.

System Information

• Keyboard: ymdk_np21
• Operating system: Arch Linux
• AVR GCC version: one inside qmkfm/qmk_cli container

• ARM GCC version: one inside qmkfm/qmk_cli container

• QMK Firmware version:
  • 0.15.3-b98280bf5 right now
  • noticed at 0.14.32 (-ish)
  • got keyboard at 2020-06-02 so not older than that

• Any keyboard related software installed?
  No

Additional information

+#define TAPPING_TOGGLE 3
+#define TAPPING_TERM   175

-BACKLIGHT_ENABLE = yes      # Enable keyboard backlight functionality
-RGBLIGHT_ENABLE = yes       # Enable keyboard RGB underglow
+BACKLIGHT_ENABLE = no       # Enable keyboard backlight functionality
+RGBLIGHT_ENABLE = no        # Enable keyboard RGB underglow
 
-LAYOUTS = ortho_6x4 numpad_6x4
+LAYOUTS = ortho_6x4
+KEY_LOCK_ENABLE = yes
+TAP_DANCE_ENABLE=yes

dmesg

I also looked to dmesg and I see messages like that:
usb 1-4.3: reset low-speed USB device number 12 using xhci_hcd

This device is indeed that keyboard:

Bus 001 Device 012: ID 594d:5021 YMDK NP21

/:  Bus 01.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/16p, 480M
    ID 1d6b:0002 Linux Foundation 2.0 root hub
    |__ Port 4: Dev 11, If 0, Class=Hub, Driver=hub/4p, 480M
        ID 05e3:0610 Genesys Logic, Inc. Hub
        |__ Port 3: Dev 12, If 1, Class=Human Interface Device, Driver=usbhid, 1.5M
            ID 594d:5021  
        |__ Port 3: Dev 12, If 0, Class=Human Interface Device, Driver=usbhid, 1.5M
            ID 594d:5021

This keyboard plugged in USB3.0 hub which is plugged into USB3.0 port. I cannot test it with 2.0 port because I don't have neither USB2.0 ports nor USB2.0 hub.