There is a significant difference between a stack-based ISA and a stack-based bytecode. In bytecode, it's fine or even a requirement to empty the stack between loop iterations. The JIT will then enregister variables across the loop as appropriate.

With x87, however, that causes extra overhead from loads and stores that's best avoided. Unused stack space can be used to cache frequently used variables, but as operations must use ST(0) as one parameter, FXCH instructions must be used to swap around variables. Matching the x87 stack state on entry and exit of the loop is tricky and compilers historically have had trouble doing it. Different FPUs also differed on the efficiency of FXCH so there were often situations where a particular arrangement would double the speed of a routine on one CPU model and halve it on another.

Not to mention the size difference as well. The JVM stack is 2^16 in size while x87 has 8.

The java compiler can practically pretend like the stack is infinite in size while a compiler dealing with x87 has to contend with spillage in all but the most trivial of algorithms.