It is indeed excellent help here.
More Infos from you would have been great like the ps2 model, usb device, and MC brand/type.
The save problem depends on your hardware so without the informations from you it would be a guessing game to say where exactly the problem is.
Long time for saving seems pretty normal for mentioned DKC3 and same applies to DKC2. The time used for saving was around 2 minutes on original Sony MC.
Modern large MC's are very slow compared to original Sony MC for saving games, this applies to PS2 games and homebrew as well.
So if using larger MC the time may be between 3 to 6 mintues.
PS2 SCPH-70004 V12 PAL + HDCOMBO + 160 GB Samsung HDD + OPL 0.9.1
PS2 SCPH-70004a V13 PAL Satin Silver
2 x Official Sony 8mb card +FMCB 1.8c + uLE 4.42b
Datel Max Memory 32mb card +FMCB 1.8b + uLE 4.42
Memor32 + Memento FW 1.2e