First of all: have you read the documentation on LRS geometries? It explains quite a bit about indexing your LRS data. Secondly:
1. Which version of Oracle are you using?
select * from v$version;
will tell you this.
2. Can you tell us the results of
select * from user_sdo_geom_metadata where table_name='TRACKPOINTS';
because LRS needs to define some dimensioning for the measure-values as well: 7.2 LRS Data Model
3. Drop your index, and create it like this:
create index spatial_idx on tablename(trackpoints) indextype is mdsys.spatial_index parameters('sdo_indx_dims=3');
This way the RTree-index only uses the X-, Y- and Z-values. See 7.3 Indexing of LRS Data.
4. If the above doesn't help you solve this, post a create table statement and some sample data that shows the same problem, so we can try to reproduce and see what is going wrong.