Under Linux they are only operable if accessed via an USB card reader.
Then they work w/o problems.
It sounds like USB read/write speeds are faster than the internal sd card reader because you say
Under Windows they work slow as heck in the system, but they work.
Hard to say what is going on because you left some important info out like what distro you are using. Whether you are using just a Window Manager or a Desktop enviorment, (Icewm,Fluxbox,Openbox,XFCE,KDE,Gnome 3?). How much cpu and ram is available also on that computer. My Ancient box I am posting from
$ inxi -F -z
System: Host: biker Kernel: 3.6.11-antix.1-486-smp i686 (32 bit)
Desktop: IceWM 1.3.7 Distro: antiX-full Edelwei▀piraten 22 August 2012
Machine: System: IBM product: 679421U
Mobo: IBM model: IBM Bios: IBM version: 20KT46AUS date: 06/04/2004
CPU: Single core Intel Pentium 4 CPU (-UP-) cache: 256 KB flags: (pae sse sse2) clocked at 1794.123 MHz
Graphics: Card: NVIDIA NV6 [Vanta/Vanta LT]
X.Org: 1.12.4 drivers: nouveau (unloaded: fbdev,vesa) Resolution: firstname.lastname@example.org
GLX Renderer: N/A GLX Version: N/A
Audio: Card: Intel 82801BA/BAM AC'97 Audio Controller driver: snd_intel8x0 Sound: ALSA ver: 1.0.25
Network: Card-1: Intel 82801BA/BAM/CA/CAM Ethernet Controller driver: e100
IF: eth0 state: down mac: <filter>
Card-2: Realtek RTL8187B Wireless 802.11g 54Mbps Network Adapter
IF: N/A state: N/A mac: N/A
Drives: HDD Total Size: 100.1GB (-) 1: id: /dev/sda model: SAMSUNG_SV6003H size: 60.1GB
2: id: /dev/sdb model: IC35L040AVVA07 size: 40.0GB
Partition: ID: / size: 25G used: 7.6G (33%) fs: ext3
Sensors: System Temperatures: cpu: 26.0C mobo: N/A
Fan Speeds (in rpm): cpu: N/A
Info: Processes: 82 Uptime: 1:50 Memory: 352.8/1134.9MB Client: Shell (bash) inxi: 1.8.45
This desktop even has a floppy drive. So having a 256GB sd flash card is a pretty nifty
toy. I be jealous.