Hello Rahul
This is normal behaviour of traceroute when you have two equal cost routes. Traceroute sends ICMP packets and since both routes are equal, it will send them via both routes.
So for your first attempt, you get the following:
Note that for the first hop, indicated by the number 1, it shows three lines. The first is the first choice, the second is the second choice and the third is the actual route that was chosen between the two. So for the first hop, 192.168.13.3, or R3 was chosen as the route.
The second hop, indicated by the number 2 also has two options, because both routes via R2 and R3 were used and there are two options to choose from once again. So either Fa 0/0 or Fa1/0 of R5 will be used as the next hop. We are told in the third line that 192.168.25.5 or Fa0/0 is used.
In the next case, you are explicitly stating that you want to use interface E1/0 or IP address 192.168.13.1 as the traceroute source:
Because you are stating this, there is no option of using the load balancing capabilities of EIGRP so only one option is indicated in each case.
Now having said all of this, if the route via R2 and R3 from R1 were UNEQUALLY load balanced (using the variance command), this wouldn’t occur. Only one option would be displayed and used. You would only see one choice for each hop. The multiple choices for each hop indicate that there is EQUAL load balancing between the R2 and R3 routes. So you should check your configuration and make sure it is load balancing UNEQUALLY using the variance command.
I hope this has been helpful!
Laz