sounds like the USB device for the card reader gets de-activated during bootup, and thus when you hot-plug, when it gets plugged in and powers up, it works again.
Which version of Windows are you running?
Acer CloudBook AO1-131 | Intel Celeron N3050 "Cherry Trail" dual | 2GB DDR3L | 32GB eMMC | Intel HD graphics
Gigabyte Brix J1900 (3x) | Intel Celeron J1900 "Bay Trail" quad | GSkill 8GB DDR3L-1600 CAS9 | 300GB Intel 320 Series SSD | Intel HD graphics
ASRock Z170 Pro4S ATX (2x) | Intel Pentium G4400 "Skylake" @ 4.455Ghz | 2x4GB Avexir DDR4-2400 | Samsung SM951 128GB M.2 AHCI SSD | AMD Radeon HD 7950 3GB