What is the source of this shape on my USB eye diagram?
This is absolutely perfect FS signal. Apparently the OP probes the signals at device end of the cable. The FS signals are unterminated by USB standard. All incoming signals (host-driven) are fine, since they are measured at destination point. However, when the device drives back an occasional handshake packet (short ACK or NAK or else), the driver hits the transmission line. Half-ampiltude signal (shouder) gets developed until the reflection from host end comes back. This is absolutely normal behavior of signals on unterminated transmission line. As I see, the round-trip delay is about 20ns, or 10ns one-way. This tells that the cable in use is about 2m long, or a standard 6ft cable. If the OP would probe the bus at host end, he would see an opposite picture. Just my 2c.