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"Could this also be because of bursty traffic?"
Yes, most likely. One of the attributes of TCP, it tends to be "bursty". If the feed to the 2.5 Gbps shaper, is greater than 2.5 Gbps, the shaper will queue traffic. How TCP responds to such queuing, depends much on the particular TCP implementation.
Some TCP implementations respond "poorly" to congestion, especially if there are drops. One of the worst cases is if the sender keeps cycling TCP slow start. If it does, there's often lots of drops and poor throughput. How network devices buffer, can impact how a TCP flow operates.
When the shaper is removed, there's still, it appears, a downstream 2.5 Gbps bottleneck, but how it impacts overrate traffic might be quite different from your shaper's impact, and hence, you obtain your 2.5 Gbps.
Although at first glance, removing the shaper appears the "better" option, that might be far from the case. The downstream bottleneck may still be dropping packets, and/or creating latency for traffic. Such might be okay, or not, but if not, you have lost management of such congestion.
The solution, is "tuning" your QoS configuration to obtain your QoS policy goals.
