Stiff manual gear shifting

My clutch pedal went down too low on my Mazda 626 Cronos 1996, and it would not bounce back as it normally should when I remove my foot, so I could no longer change gears. My mechanic told me it needed a new clutch master cylinder. After he replaced it I noticed the clutch pedal was low: I could change gears and the pedal would bounce back, but lower than its normal position. My mechanic told me I should not worry. I drove the car a few days and for short distances without problems. A week after the replacement of the master clutch cylinder, I noticed when I started my car in the morning that the rear gear was stiff, and so were other gears as I moved forward. But little by little, gear shifting became smooth as usual. The next time I drove my car was 2 days afterwards. This time gear shifting was even much stiffer. It took some driving and difficult gear shifting before gear shifting became smooth. So what is wrong? Was the clutch master cylinder not installed properly? Thank you.