You're probably using one of the unsigned variants like:
cmp eax, ebx
jb lesser
There are equivalents for checking signed numbers against each other, such as:
cmp eax, ebx
jl lesser
This link gives a good run down on the jump variations, including their signed-ness and the flags they check, partially copied here for self-containment:
Instruction Jump if ... Signed? Flags
----------- ----------- -------- -----
JO overflow OF=1
JNO not overflow OF=0
JS sign SF=1
JNS not sign SF=0
JE/JZ equal
zero ZF=1
JNE/JNZ not-equal
not-zero ZF=0
JB/JNAE/JC below
not-above-or-equal
carry unsigned CF=1
JNB/JAE/JNC not-below
above-or-equal
no-carry unsigned CF=0
JBE/JNA below-or-equal
not-above unsigned CF=1 or ZF=1
JA/JNBE above
not-below-or-equal unsigned CF=0 and ZF=0
JL/JNGE less
not-greater-or-equal signed SF<>OF
JGE/JNL greater-or-equal
not-less signed SF=OF
JLE/JNG less-or-equal
not-greater signed ZF=1 or SF<>OF
JG/JNLE greater
not-less-or-equal signed ZF=0 and SF=OF
JP/JPE parity
parity-even PF=1
JNP/JPO not-parity
parity-odd PF=0
JCXZ/JECXZ CX register is zero
ECX register is zero
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